Variant report

Variant	rs10264803
Chromosome Location	chr7:3516425-3516426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1010002	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10155878	0.83[ASN][1000 genomes]
rs10226719	1.00[JPT][hapmap]
rs10228744	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10235080	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10235617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10237328	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs10238338	1.00[YRI][hapmap]
rs10245071	1.00[JPT][hapmap]
rs10250929	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10256447	0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs10258943	1.00[YRI][hapmap]
rs10266927	0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs10274012	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10282346	0.85[ASN][1000 genomes]
rs10485876	1.00[JPT][hapmap]
rs10951207	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10951265	1.00[JPT][hapmap]
rs11760339	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs11766767	1.00[JPT][hapmap]
rs11768609	1.00[JPT][hapmap]
rs11770829	1.00[JPT][hapmap]
rs11773388	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12531560	1.00[JPT][hapmap]
rs12535467	1.00[JPT][hapmap]
rs12539289	1.00[JPT][hapmap]
rs12539805	1.00[JPT][hapmap]
rs12540148	1.00[JPT][hapmap]
rs12673946	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12701005	1.00[JPT][hapmap]
rs12701014	1.00[JPT][hapmap]
rs13223065	0.82[JPT][hapmap]
rs13223852	0.82[JPT][hapmap]
rs13240060	0.85[JPT][hapmap]
rs13242531	1.00[JPT][hapmap]
rs1403162	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[YRI][hapmap]
rs17320730	1.00[JPT][hapmap]
rs17751535	1.00[YRI][hapmap]
rs1922016	1.00[JPT][hapmap]
rs2033441	1.00[JPT][hapmap]
rs2099302	1.00[JPT][hapmap]
rs2341584	0.82[JPT][hapmap]
rs2341586	0.82[JPT][hapmap]
rs2614950	0.82[JPT][hapmap]
rs2614955	1.00[JPT][hapmap]
rs2614957	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2705609	0.80[GIH][hapmap];1.00[JPT][hapmap]
rs28484810	0.83[ASN][1000 genomes]
rs28544580	0.83[ASN][1000 genomes]
rs2880085	1.00[JPT][hapmap]
rs2880087	1.00[JPT][hapmap]
rs3919653	1.00[JPT][hapmap]
rs4236325	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs4342491	1.00[JPT][hapmap]
rs4363091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4719964	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4722903	0.82[JPT][hapmap]
rs4723001	1.00[JPT][hapmap]
rs7779391	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs956393	1.00[JPT][hapmap]
rs9648355	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs968775	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020764	chr7:3348458-3554820	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv538662	chr7:3348458-3554820	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2764026	chr7:3365002-3618361	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1015296	chr7:3381813-3560401	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv528715	chr7:3451251-3598581	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv887332	chr7:3455249-3521000	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv605902	chr7:3464896-3598581	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv605903	chr7:3472721-3527925	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv887333	chr7:3475716-3542488	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv869723	chr7:3482682-3566293	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv464270	chr7:3490865-3581357	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv605904	chr7:3490865-3581357	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1027426	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv538672	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1034716	chr7:3512406-3616155	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10264803	GNA12	cis	lymphoblastoid	seeQTL
rs10264803	LOC389458	cis	cerebellum	SCAN
rs10264803	MAD1L1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3491200-3526600	Weak transcription	Pancreas	Pancrea
2	chr7:3502000-3521200	Weak transcription	Aorta	Aorta
3	chr7:3506200-3521000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:3512800-3522400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:3513000-3522000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:3516000-3521000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:3516000-3522200	Weak transcription	Fetal Lung	lung
8	chr7:3516400-3516600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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