SNP linked to Gene <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=3055">HCK</a>(geneID:3055) Via Contig Annotation

SNP linked to Gene HCK(geneID:3055) Via Contig Annotation

Gene Model (mRNA alignment) information from genome sequence

Total gene model (contig mRNA transcript):				2
mrna	transcript	protein	mrna orientation	Contig	Contig Label	List SNP
NM_002110.2	plus strand	NP_002101.2	forward	NT_028392.5	reference	<- currently shown
NM_002110.2	minus strand	NP_002101.2	reverse	NW_001838664.2	HuRef	View snp on GeneModel

Include clinically associated

in gene region cSNP has frequency double hit

gene model (contig mRNA transcript):	Contig Label	Contig	mrna	protein	mrna orientation	transcript	snp count
gene model (contig mRNA transcript):	reference	NT_028392.5	NM_002110.2	NP_002101.2	forward	plus strand	286, all

		Color Legend

Region	Contig position	mRNA pos	dbSNP rs# cluster id	Hetero- zygosity	3D	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos
5' near gene	834533		rs6058519	N.D.		5' near gene	A/C
	835456		rs17093775	0.071		5' near gene	A/G
	835475		rs57701871	N.D.		5' near gene	A/G
	835522		rs1004910	0.188		5' near gene	A/C
	835588		rs17093784	N.D.		5' near gene	A/G
	835900		rs13043040	N.D.		5' near gene	G/T

exon_1	836244	96	rs41303795	N.D.		5' UTR	C/G
exon_1	836320	172				start codon				1

intron_1	836517		rs11699670	N.D.		intron	A/G
	836687		rs6061134	N.D.		intron	-/C/G/GC
	836687		rs58976342	N.D.		intron	-/C
	836692		rs11447150	N.D.		intron	-/T
	836702		rs35592300	N.D.		intron	-/T
	837431		rs6121325	N.D.		intron	G/T
	837621		rs57242437	N.D.		intron	A/G
	837653		rs6142598	N.D.		intron	A/G
	837667		rs62207270	N.D.		intron	A/T
	837717		rs6142599	N.D.		intron	A/G
	837890		rs62207271	N.D.		intron	C/T
	837902		rs34507358	N.D.		intron	-/T
	838084		rs59995765	N.D.		intron	C/T
	838419		rs58415391	N.D.		intron	-/AAAAAAAAAAAAAAAAAAA
	838432		rs6121326	N.D.		intron	G/T
	838520		rs6061135	N.D.		intron	G/T
	838611		rs4359727	N.D.		intron	A/G
	838793		rs6058520	N.D.		intron	C/T
	838963		rs61456149	N.D.		intron	-/T
	839607		rs6121327	N.D.		intron	A/G
	839687		rs6121328	0.126		intron	C/T
	840079		rs7263906	N.D.		intron	A/G
	840136		rs34143132	N.D.		intron	-/C
	840557		rs6061136	0.150		intron	G/T
	841166		rs11478318	N.D.		intron	-/C
	841203		rs6061137	N.D.		intron	A/G
	841286		rs6061138	N.D.		intron	A/G
	841334		rs6142601	N.D.		intron	A/C
	841398		rs6061139	N.D.		intron	A/G
	841430		rs6061140	N.D.		intron	A/G
	841574		rs7266178	0.110		intron	A/G
	841888		rs6061141	N.D.		intron	C/T
	842051		rs6058522	0.296		intron	C/T
	842126		rs11475545	N.D.		intron	-/A
	842135		rs3833316	N.D.		intron	-/A
	842230		rs55726906	N.D.		intron	A/C
	842260		rs11697528	N.D.		intron	C/T
	842281		rs6061142	N.D.		intron	G/T
	842429		rs11480270	N.D.		intron	-/A
	842439		rs11472244	N.D.		intron	-/AG
	842440		rs33978689	N.D.		intron	-/AG
	842501		rs62207272	N.D.		intron	A/C
	842509		rs11472245	N.D.		intron	-/CACA
	842511		rs34307504	N.D.		intron	-/ACAC
	842532		rs60349531	N.D.		intron	-/CACA
	842535		rs60740993	N.D.		intron	-/CACACA
	843174		rs11272727	N.D.		intron	-/CTTCCTTCCTTCCTTC
	843191		rs885495	N.D.		intron	-/C/T/TTCCTTCCTTCC
	843192		rs35328948	N.D.		intron	-/TTCCTTCCTTCC
	843304		rs6121329	N.D.		intron	C/T
	843314		rs6119756	N.D.		intron	C/T
	843322		rs10644991	N.D.		intron	-/TCTT
	843327		rs3073296	N.D.		intron	-/CTTT
	843408		rs6089157	N.D.		intron	C/T
	843410		rs56390911	N.D.		intron	C/T
	843413		rs7509404	N.D.		intron	C/T
	843414		rs10557922	N.D.		intron	-/TTT
	843479		rs6061143	N.D.		intron	C/T
	843879		rs17379736	0.041		intron	C/G
	844015		rs6061144	0.005		intron	A/G
	844623		rs7354524	N.D.		intron	G/T
	844670		rs4911541	0.400		intron	C/T
	844793		rs11269818	N.D.		intron	-/GAAGAAAGGAAGGAA
	844804		rs11267532	N.D.		intron	-/GGAAGAAGAAAGGAA
	844917		rs4911542	N.D.		intron	C/T
	845094		rs2001413	N.D.		intron	C/G
	845166		rs6579320	N.D.		intron	C/T
	845348		rs6119757	N.D.		intron	C/T
	845359		rs8114692	N.D.		intron	G/T
	845515		rs6142602	N.D.		intron	A/G
	845622		rs6121330	N.D.		intron	C/T
	845658		rs7265833	N.D.		intron	A/G
	845753		rs6119758	N.D.		intron	A/G
	845841		rs11309258	N.D.		intron	-/T
	845926		rs1987960	N.D.		intron	C/T
	846194		rs6121331	N.D.		intron	C/G
	846395		rs6058523	N.D.		intron	A/G
	846578		rs3787366	N.D.		intron	A/G
	846664		rs17093788	0.432		intron	A/G
	846750		rs7268039	0.005		intron	A/G
	847123		rs58814478	N.D.		intron	A/G
	847618		rs17093790	0.041		intron	C/G
	847662		rs6089158	0.214		intron	A/T
	847674		rs58250655	N.D.		intron	A/T
	847813		rs6061145	N.D.		intron	A/G
	847913		rs58620860	N.D.		intron	-/TTTT
	847914		rs58755368	N.D.		intron	-/TTT
	847930		rs6089159	N.D.		intron	G/T
	848469		rs3787367	0.141		intron	A/G
	849108		rs7269735	0.051		intron	C/T
	849730		rs6061146	N.D.		intron	A/G
	849908		rs36019250	N.D.		intron	-/A
	849926		rs6089160	N.D.		intron	A/G
	850003		rs6089161	N.D.		intron	A/G
	850043		rs6089162	N.D.		intron	C/G
	850199		rs35827345	N.D.		intron	-/C
	850225		rs6061147	N.D.		intron	G/T
	850226		rs6061148	N.D.		intron	-/A/T/TTT
	850226		rs60044994	N.D.		intron	-/TTTTTGA
	850228		rs10672322	N.D.		intron	-/GA
	850229		rs35269304	N.D.		intron	-/GA
	850521		rs36060537	N.D.		intron	-/T
	850770		rs17093799	0.014		intron	A/T
	851314		rs58948864	N.D.		intron	C/T
	851426		rs11482239	N.D.		intron	-/T
	851427		rs35100827	N.D.		intron	-/T
	851447		rs57147819	N.D.		intron	-/T
	851585		rs34422885	N.D.		intron	-/G
	851707		rs11696958	N.D.		intron	C/T
	851895		rs35305942	N.D.		intron	A/T
	852117		rs35710845	N.D.		intron	-/C
	852155		rs6089163	N.D.		intron	C/T
	852221		rs6579321	N.D.		intron	A/T
	852230		rs28712323	N.D.		intron	A/T
	852285		rs11308622	N.D.		intron	-/T
	852293		rs10719271	N.D.		intron	-/T
	852649		rs7275160	N.D.		intron	C/G
	852816		rs34188764	N.D.		intron	-/G
	853215		rs17093805	0.028		intron	A/G
	853711		rs6089164	0.326		intron	A/G
	854669		rs7354349	0.260		intron	A/G
	854773		rs7267655	N.D.		intron	A/G
	854779		rs7264792	N.D.		intron	C/G
	855428		rs6061151	N.D.		intron	A/G

exon_2	855613	290	rs6089165	N.D.		missense	T	Ile [I]	2	40
						contig reference	C	Thr [T]	2	40
	855624	301	rs56029200	N.D.		missense	A	Thr [T]	1	44
						contig reference	G	Ala [A]	1	44
	855629	306	rs34774796	0.145		synonymous	T	Ser [S]	3	45
						contig reference	C	Ser [S]	3	45

intron_2	855907		rs6142603	N.D.		intron	C/T
	856233		rs59489790	N.D.		intron	C/T
	856458		rs3838038	N.D.		intron	-/T/TAAAAAAAA
	856678		rs6142604	N.D.		intron	A/G
	856713		rs6061152	N.D.		intron	C/T
	856915		rs62207273	N.D.		intron	A/G
	856951		rs62207274	N.D.		intron	C/T

exon_3	857222	363	rs34513177	0.025		synonymous	C	Asn [N]	3	64
						contig reference	T	Asn [N]	3	64

intron_3	857303		rs7264938	0.028		intron	A/G
	857344		rs2297303	0.024		intron	A/T
	857361		rs7270725	N.D.		intron	C/T
	857384		rs60766411	N.D.		intron	C/G
	857389		rs2297304	0.380		intron	A/G
	857396		rs2297305	N.D.		intron	A/G

exon_4	857666	453	rs2227967	0.059	Yes	synonymous	T	His [H]	3	94
						contig reference	C	His [H]	3	94
	857677	464	rs6089166	N.D.		missense	T	Ile [I]	2	98
						contig reference	G	Ser [S]	2	98
	857697	484	rs55722810	N.D.		missense	T	Leu [L]	1	105
						contig reference	A	Met [M]	1	105

intron_4	857939		rs60000242	N.D.		intron	A/C
	857999		rs57810433	N.D.		intron	C/T
	858011		rs17093809	0.028		intron	C/T
	858327		rs60169743	N.D.		intron	G/T
	858339		rs6061153	0.497		intron	G/T
	858366		rs6061154	0.235		intron	C/G

intron_5	858885		rs60758860	N.D.		intron	A/C
	858897		rs3746601	0.498		intron	A/C
	858929		rs3746602	N.D.		intron	A/G
	858975		rs6089167	N.D.		intron	G/T
	859200		rs56097656	N.D.		intron	A/C
	859262		rs6121334	N.D.		intron	C/T
	859518		rs17093810	0.139		intron	C/T
	859601		rs60416489	N.D.		intron	-/TCAT
	859637		rs56660439	N.D.		intron	-/CATC
	859973		rs442268	N.D.		intron	A/T
	859975		rs381619	N.D.		intron	C/T
	860168		rs6089168	N.D.		intron	C/T
	860281		rs242598	N.D.		intron	C/T
	860466		rs242599	0.237		intron	A/G
	861102		rs6119760	N.D.		intron	C/T
	861433		rs59721765	N.D.		intron	-/GTTTT
	861655		rs242600	N.D.		intron	A/G
	861728		rs6119761	0.199		intron	C/T
	861926		rs242601	N.D.		intron	G/T
	862229		rs173355	N.D.		intron	C/T
	862775		rs6087815	N.D.		intron	A/G
	862777		rs35088805	N.D.		intron	C/G
	863040		rs242602	0.469		intron	C/T
	863151		rs242603	0.481		intron	C/T

intron_6	863782		rs3746603	0.020		intron	A/G
	864343		rs242604	N.D.		intron	C/T
	864636		rs242605	N.D.		intron	C/G
	864725		rs242606	0.500		intron	A/G
	865018		rs35091816	N.D.		intron	-/A
	865195		rs17093812	0.028		intron	C/G
	865210		rs58663849	N.D.		intron	C/T
	865236		rs35315557	N.D.		intron	-/G
	865703		rs34022054	N.D.		intron	-/G
	866393		rs1883882	N.D.		intron	C/T
	866688		rs6121335	0.278		intron	C/T
	867532		rs59388669	N.D.		intron	A/C
	867736		rs6142605	N.D.		intron	A/G

exon_7	867901	816	rs6058524	N.D.	Yes	synonymous	T	Thr [T]	3	215
						contig reference	C	Thr [T]	3	215

intron_7	867967		rs242607	0.274		intron	C/T
	868021		rs6121336	N.D.		intron	C/T

intron_8	868916		rs57726996	N.D.		intron	C/T
	868928		rs242608	0.320		intron	C/T
	869205		rs60902201	N.D.		intron	C/T
	869516		rs242609	0.214		intron	C/T
	869784		rs242610	0.422		intron	C/T
	870040		rs62204979	N.D.		intron	C/T
	870070		rs242611	0.434		intron	A/G
	870313		rs59055761	N.D.		intron	G/T
	870314		rs59047893	N.D.		intron	C/G
	870348		rs8121958	N.D.		intron	C/G

exon_9	870527	1011	rs6061156	N.D.	Yes	synonymous	T	Thr [T]	3	280
						contig reference	C	Thr [T]	3	280
	870680	1164	rs34436416	0.027	Yes	synonymous	T	Ile [I]	3	331
						contig reference	C	Ile [I]	3	331

intron_9	870710		rs910185	0.183		intron	A/G
	871002		rs6142606	N.D.		intron	G/T
	871031		rs35802892	N.D.		intron	-/G
	871057		rs35904270	N.D.		intron	-/C
	871541		rs242612	N.D.		intron	A/T
	871623		rs242613	N.D.		intron	A/G
	871768		rs242614	N.D.		intron	A/G
	871906		rs242615	N.D.		intron	C/G
	872408		rs2223785	N.D.		intron	C/T

intron_10	872853		rs35228115	N.D.		intron	-/G
	872868		rs17093823	0.028		intron	A/G
	873141		rs11906504	N.D.		intron	C/G
	873150		rs57144947	N.D.		intron	A/G
	873208		rs10599801	N.D.		intron	-/ATC
	873209		rs34946961	N.D.		intron	-/ATC
	873300		rs6089170	0.496		intron	C/T
	874206		rs7347740	N.D.		intron	A/G
	874644		rs17259459	0.183		intron	C/T
	875074		rs2269052	0.152		intron	A/G
	875713		rs5841096	N.D.		intron	-/A
	875718		rs34200572	N.D.		intron	-/A
	876012		rs35526857	N.D.		intron	G/T
	876305		rs59179691	N.D.		intron	G/T
	876317		rs926687	0.494		intron	G/T
	876430		rs926688	0.495		intron	G/T
	876547		rs6119762	N.D.		intron	C/T
	877036		rs62204981	N.D.		intron	C/T
	877123		rs62204982	N.D.		intron	A/G
	877187		rs17093827	0.082		intron	A/G
	877377		rs7260985	0.028		intron	C/T
	877380		rs12329552	N.D.		intron	C/G
	877386		rs11167298	N.D.		intron	-/C/G/GT/GTGT
	877386		rs28647760	N.D.		intron	C/G
	877403		rs980367	N.D.		intron	G/T
	877409		rs5841097	N.D.		intron	-/TG
	877416		rs3073297	N.D.		intron	-/GT
	877417		rs35596683	N.D.		intron	-/TG
	877418		rs58517209	N.D.		intron	-/TG
	877546		rs11697159	N.D.		intron	A/C
	877635		rs980368	0.495		intron	A/G

intron_11	878091		rs6121337	0.492		intron	C/T
	878188		rs60782500	N.D.		intron	A/G
	878450		rs35263404	N.D.		intron	-/C
	878646		rs6058525	N.D.		intron	A/G
	878663		rs6142607	N.D.		intron	A/G
	878863		rs6089171	0.186		intron	C/T
	879513		rs34711233	N.D.		intron	-/G
	879786		rs61586741	N.D.		intron	-/ATTTATTTATTTATTT
	880253		rs62204983	N.D.		intron	A/G
	880319		rs13038345	N.D.		intron	C/G
	880415		rs55905450	N.D.		intron	-/AA
	880416		rs59015442	N.D.		intron	-/A
	880880		rs6089174	0.475		intron	A/T
	880921		rs6089175	N.D.		intron	A/T
	881248		rs34099113	N.D.		intron	-/G
	881800		rs9679931	N.D.		intron	A/G
	882324		rs6121338	N.D.		intron	A/G
	882515		rs12481708	0.168		intron	C/T
	882776		rs3833317	N.D.		intron	-/G

intron_12	883157		rs35974379	N.D.		intron	C/T
	883257		rs11468396	N.D.		intron	-/TTT
	883377		rs34007778	N.D.		intron	-/T
	883806		rs5841098	N.D.		intron	-/T
	883807		rs5841099	N.D.		intron	-/T
	883811		rs34071977	N.D.		intron	-/T
	884325		rs35316298	N.D.		intron	-/C
	884371		rs34881114	N.D.		intron	-/G
	884832		rs6089177	0.017		intron	C/T
	884936		rs6087816	0.207		intron	A/G
	885015		rs8122892	N.D.		intron	G/T

exon_13	885338	1676	rs17093828	0.011		missense	A	Gln [Q]	2	502
						contig reference	C	Pro [P]	2	502

3' near gene	886016		rs11480322	N.D.		3' near gene	-/A
	886017		rs33993055	N.D.		3' near gene	-/A
	886021		rs11480894	N.D.		3' near gene	-/A
	886022		rs34609613	N.D.		3' near gene	-/A
	886024		rs11482586	N.D.		3' near gene	-/A
	886032		rs34088834	N.D.		3' near gene	-/A

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Revised: May 25, 2006 1:38 PM .