Reference SNP(refSNP) Cluster Report: rs152524

Reference SNP(refSNP) Cluster Report: rs152524

refSNP ID: rs152524
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_000800.2:c.169+1135T>C
NM_033136.1:c.169+1135T>C
NM_033137.1:c.169+1135T>C
NT_029289.10:g.3155316A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5578040 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs152524 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss245392	KWOK\|OVLP-000621-30358	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	06/30/00	10/10/03	79	Genomic	89 %
ss323716	KWOK\|OVLP-000621-31366	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	06/30/00	10/10/03	79	Genomic	99 %
ss498997	SC_JCM\|AC016560.5_182094	rev/B	C/T	accctcagatgcacaggtaatggggatgga	gctggcgtttacacgaggtgacgttgttcc	07/12/00	10/10/03	80	Genomic	unknown
ss1273676	KWOK\|OVLP-000804-403431	rev/B	C/T	accctcagatgcacaggtaatggggatgga	gctggcgtttacacgaggtgacgttgttcc	09/02/00	10/10/03	86	Genomic	94 %
ss1284241	KWOK\|OVLP-000804-407113	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	09/02/00	10/10/03	86	Genomic	87 %
ss1320171	TSC-CSHL\|TSC0161514	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	09/06/00	04/07/04	86	Genomic	95 %
ss1750942	KWOK\|OVLP-000925-530735	rev/B	C/T	accctcagatgcacaggtaatggggatgga	gctggcgtttacacgaggtgacgttgttcc	10/05/00	10/10/03	87	Genomic	94 %
ss5578040	TSC-CSHL\|TSC0271258	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	09/21/02	10/25/06	110	Genomic	unknown
ss11723640	WI_SSAHASNP\|chr5.NT_029289.9_3155317	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	07/03/03	10/10/03	116	Genomic	unknown
ss23140713	EGP_SNPS\|FGF1-075227	rev/B	C/T	accctcagatgcacaggtaatggggatgga	gctggcgtttacacgaggtgacgttgttcc	04/22/04	04/28/04	126	Genomic	unknown
ss24621983	PERLEGEN\|afd3321242	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	08/10/04	09/13/04	123	Genomic	unknown
ss65775381	ILLUMINA\|Human1-rs152524	fwd/B	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	10/10/06	10/10/06	127	Genomic	unknown
ss66861199	EGP_SNPS\|FGF1_075227	rev/B	C/T	accctcagatgcacaggtaatggggatgga	gctggcgtttacacgaggtgacrttgttcc	11/09/06	12/16/06	127	Genomic	unknown
ss74879541	ILLUMINA\|ILMN_Human_1M_rs152524	fwd/T	A/G	ggaacaacgtcacctcgtgtaaacgccagc	tccatccccattacctgtgcatctgagggt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 AGCTTGTTCG TGTTGTGTGG GGCAGATCAC GTGAGTTGTG TATCATGCCT GACACAATGG
 ACTACAATCT AAGTTTGCTA ATTTGCAGTG AATATTGCTT ATGTATGCTA TTTAACAAAC
 TAGAGTCTTT TTTTTTTGCC TCATTCTGAC ACCTGTTTTT CACTGAGTAT AAGACATTCA
 GCAAGCCCAT TTGAAGATAA GCCATCAAAA CAAAGCCCAA AAGAGCTAAT TCTGCAGCTG
 CAAGCCCCAG CCTCAGCCTT CCTGCTCCTC ATCTCCAGGG TCTGTGCAGT GGGTGGGGAG
 GAAGGAACAA CGTCACCTCG TGTAAACGCC AGC
 R
 TCCATCCCCA TTACCTGTGC ATCTGAGGGT ACAGCGTGAG CACCAGCGAA GTGGTCATTT
 GTTCTTAGAG CCTGCAACCT CTGGTGCATG GTCCATGAAT AATTAAGACC ACCTGATGTA
 TAAACCATCA TGTCAAAGTG AGTGTTTTGC ATTGCATTTT GAAGCCAGTC CTACAGAAAC
 TTCCTTCCTG CCTGTCTTCT TCTATGTCTC CTGATTTTCC TTCTCTTGAT TTGTGGCAAG
 TTTGACTCTT GAGATTGCTG ACCCTCTAAG CAGGGACTGG ATCTGACTTT

GeneView

GeneView via analysis of contig annotation: FGF1 fibroblast growth factor 1 (acidic)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_029289->NM_000800

function

reference

NT_029289->NM_033136

function

reference

NT_029289->NM_033137

function

HuRef

NW_001838953->NM_000800

function

HuRef

NW_001838953->NM_033136

function

HuRef

NW_001838953->NM_033137

function

Celera

NW_922784->NM_000800

function

Celera

NW_922784->NM_033136

function

Celera

NW_922784->NM_033137

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_029289->NM_000800->NP_000791	3155316	reverse	intron

reference	NT_029289->NM_033136->NP_149127	3155316	reverse	intron

reference	NT_029289->NM_033137->NP_149128	3155316	reverse	intron

HuRef	NW_001838953->NM_000800->NP_000791	13142130	forward	intron

HuRef	NW_001838953->NM_033136->NP_149127	13142130	forward	intron

HuRef	NW_001838953->NM_033137->NP_149128	13142130	forward	intron

Celera	NW_922784->NM_000800->NP_000791	15701726	reverse	intron

Celera	NW_922784->NM_033136->NP_149127	15701726	reverse	intron

Celera	NW_922784->NM_033137->NP_149128	15701726	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs152524 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838953.2	13142130	137140115	minus	T	alt_assembly_8	HuRef	HuRef	view	333
5	NW_922784.1	15701726	138073710	plus	A	alt_assembly_1	Celera	Celera	view	333
5	NT_029289.10	3155316	141972573	plus	A	ref_assembly	reference	reference	view	333

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029289 AC010489 AC010489.4 AC016560.6

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC005370.1 AC010489.4 NC_000005.8	AC016560.9 AC091822.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1320171	TSC_42_AA		75	AF					0.366	0.634

	TSC_42_C		84	AF					0.583	0.417

	TSC_42_A		83	AF					0.307	0.693

ss23140713	PDR90	Global	162	IG	0.383	0.420	0.198	0.251	0.593	0.407

ss24621983	AFD_EUR_PANEL	European	48	IG	0.292	0.417	0.292	0.439	0.500	0.500

	AFD_AFR_PANEL	African American	46	IG	0.217	0.435	0.348	0.584	0.435	0.565

	AFD_CHN_PANEL	Asian	48	IG	0.167	0.417	0.417	0.655	0.375	0.625

ss5578040	HapMap-CEU	European	116	IG	0.448	0.362	0.190	0.655	0.629	0.371

	HapMap-HCB	Asian	90	IG	0.156	0.511	0.333	1.000	0.411	0.589

	HapMap-JPT	Asian	88	IG	0.159	0.386	0.455	0.273	0.352	0.648

	HapMap-YRI	Sub-Saharan African	118	IG	0.034	0.610	0.356	0.005	0.339	0.661

ss66861199	HSP_GENO_PANEL		118	IG	0.458	0.407	0.136	0.479	0.661	0.339

	CEU_GENO_PANEL	European	120	IG	0.433	0.367	0.200	0.100	0.617	0.383

	AAM_GENO_PANEL	African American	122	IG	0.148	0.475	0.377	1.000	0.385	0.615

	CHB_GENO_PANEL	Asian	90	IG	0.156	0.511	0.333	0.752	0.411	0.589

	YRI_GENO_PANEL	Sub-Saharan African	120	IG	0.033	0.617	0.350	0.005	0.342	0.658

	JPT_GENO_PANEL	Asian	90	IG	0.156	0.400	0.444	0.403	0.356	0.644