Variant report

Variant	rs12053817
Chromosome Location	chr3:61182765-61182766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1001788	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10049007	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10049287	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10049452	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10049454	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11130821	0.88[EUR][1000 genomes]
rs11130822	0.87[EUR][1000 genomes]
rs11130826	0.83[EUR][1000 genomes]
rs11707984	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11712122	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11720254	0.82[EUR][1000 genomes]
rs12492551	0.83[EUR][1000 genomes]
rs12492939	0.96[EUR][1000 genomes]
rs12635622	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13099397	0.90[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs13320646	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13323296	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1371095	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1470035	0.82[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs1473644	0.80[ASN][1000 genomes]
rs1550343	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1554599	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1554601	1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17064630	0.87[EUR][1000 genomes]
rs1866433	1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1866434	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1880213	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1916800	0.82[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs1916801	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs1916802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1966136	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap]
rs1969420	0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1980308	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs1980309	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs1980310	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs1980311	0.84[EUR][1000 genomes]
rs2118811	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2365389	0.80[EUR][1000 genomes]
rs2886377	1.00[ASW][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35198002	0.87[EUR][1000 genomes]
rs4309721	0.89[ASW][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4535219	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4605537	0.83[EUR][1000 genomes]
rs4688295	0.93[ASN][1000 genomes]
rs4688310	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688334	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4688352	0.81[EUR][1000 genomes]
rs4688354	0.82[EUR][1000 genomes]
rs4688355	0.82[EUR][1000 genomes]
rs4688379	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56076618	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61275795	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445196	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6445200	0.84[GIH][hapmap]
rs6787292	0.87[EUR][1000 genomes]
rs6787313	0.85[EUR][1000 genomes]
rs6787511	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6807748	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs71296711	0.83[EUR][1000 genomes]
rs753661	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7631101	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7631246	0.89[ASW][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7636682	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7641177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7647122	0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7653719	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9811478	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9814044	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9816087	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9819588	0.94[ASW][hapmap];0.94[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9832387	0.82[EUR][1000 genomes]
rs9832404	0.81[EUR][1000 genomes]
rs9839082	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9844741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846073	0.82[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs9850114	0.83[EUR][1000 genomes]
rs9850125	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9851485	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9855716	0.82[JPT][hapmap]
rs9857606	0.87[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9861713	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9871451	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9871598	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9882800	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1014142	chr3:61136874-61184782	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv997718	chr3:61176349-61222975	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61161000-61186000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:61172400-61203000	Weak transcription	Pancreas	Pancrea
4	chr3:61176200-61183200	Weak transcription	Lung	lung
5	chr3:61177600-61185800	Weak transcription	Fetal Intestine Small	intestine
6	chr3:61179000-61182800	Enhancers	HepG2	liver
7	chr3:61181200-61185600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:61181400-61183600	Weak transcription	Fetal Intestine Large	intestine
9	chr3:61181400-61186400	Weak transcription	GM12878-XiMat	blood
10	chr3:61181400-61187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:61182600-61182800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:61182600-61182800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links