Variant report

Variant	rs9524268
Chromosome Location	chr13:94543694-94543695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10775112	0.92[CEU][hapmap]
rs11617930	0.92[CEU][hapmap]
rs12876318	0.92[CEU][hapmap]
rs1330468	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1411507	0.92[CEU][hapmap]
rs1411510	0.92[CEU][hapmap]
rs1411513	0.92[CEU][hapmap];0.82[CHD][hapmap];0.84[EUR][1000 genomes]
rs1888230	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1888231	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1888232	0.87[EUR][1000 genomes]
rs1983987	1.00[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1983988	0.82[EUR][1000 genomes]
rs2150124	0.91[CEU][hapmap]
rs2183426	0.92[CEU][hapmap]
rs2183430	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2210110	0.87[EUR][1000 genomes]
rs2892667	0.91[CEU][hapmap]
rs3759422	0.92[CEU][hapmap]
rs3759423	0.92[CEU][hapmap]
rs4274304	0.92[CEU][hapmap]
rs4326909	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4486746	0.92[CEU][hapmap]
rs7317037	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7317144	0.92[CEU][hapmap]
rs7320107	0.83[EUR][1000 genomes]
rs7320571	0.92[CEU][hapmap]
rs7326965	0.87[EUR][1000 genomes]
rs7329264	1.00[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs7330202	0.92[CEU][hapmap]
rs7983205	0.86[EUR][1000 genomes]
rs7986675	0.81[EUR][1000 genomes]
rs7988628	0.95[CEU][hapmap]
rs7989528	1.00[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7991274	0.91[CEU][hapmap]
rs7999251	0.92[CEU][hapmap]
rs8001981	0.87[EUR][1000 genomes]
rs885192	0.92[CEU][hapmap]
rs928189	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9284274	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9301912	0.80[EUR][1000 genomes]
rs9301913	1.00[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs9301914	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9301916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516286	0.91[CEU][hapmap]
rs9516289	0.92[CEU][hapmap]
rs9516301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9516302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9516306	0.81[EUR][1000 genomes]
rs9516308	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9524217	0.92[CEU][hapmap]
rs9524226	0.91[CEU][hapmap]
rs9524227	0.92[CEU][hapmap]
rs9524228	0.92[CEU][hapmap]
rs9524230	0.92[CEU][hapmap]
rs9524233	0.92[CEU][hapmap]
rs9524247	0.80[EUR][1000 genomes]
rs9524249	0.91[CEU][hapmap];0.81[MEX][hapmap]
rs9524252	0.86[EUR][1000 genomes]
rs9524253	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9524254	1.00[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs9524257	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9524262	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9524263	0.92[CEU][hapmap];0.88[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs9524264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9524265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9524272	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524274	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556326	0.92[CEU][hapmap]
rs9556328	0.92[CEU][hapmap]
rs9556334	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs9561444	0.92[CEU][hapmap]
rs9561448	0.92[CEU][hapmap]
rs9561449	0.92[CEU][hapmap]
rs9561458	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9589837	0.92[CEU][hapmap]
rs9589841	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9589842	0.92[CEU][hapmap];0.81[CHD][hapmap]
rs9589848	0.95[CEU][hapmap]
rs991431	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs991596	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs991597	0.84[EUR][1000 genomes]
rs996920	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs996921	0.92[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1045230	chr13:94277683-94764671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv832684	chr13:94379507-94550853	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv430598	chr13:94490519-94546599	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3321835	chr13:94541851-94546449	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9524268	GPC6	cis	Artery Aorta	GTEx

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94543600-94544200	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links