Variant report

Variant	rs12629848
Chromosome Location	chr3:23304450-23304451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1013460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1027379	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1032499	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs11129113	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11129116	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11129119	0.82[JPT][hapmap]
rs11708117	0.89[ASN][1000 genomes]
rs11708176	0.85[ASN][1000 genomes]
rs11717397	0.82[ASN][1000 genomes]
rs11720461	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11920019	0.87[ASN][1000 genomes]
rs12330262	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12330479	0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12493361	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12496983	0.82[ASN][1000 genomes]
rs12497974	0.88[ASN][1000 genomes]
rs13074192	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13080261	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13080401	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13081371	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13321359	0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs13326048	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1495131	0.84[CEU][hapmap];0.91[ASN][1000 genomes]
rs1532355	0.89[ASN][1000 genomes]
rs1552930	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1692617	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs1692651	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1695171	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs17012812	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17012869	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874235	0.86[ASN][1000 genomes]
rs1973400	0.92[ASN][1000 genomes]
rs2055154	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2172828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359759	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2359763	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs3104243	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs34919006	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4241511	0.81[CEU][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4488778	0.89[ASN][1000 genomes]
rs4858062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858064	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858071	0.80[ASN][1000 genomes]
rs4858483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858484	0.81[CEU][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858491	0.85[ASN][1000 genomes]
rs4858492	0.83[ASN][1000 genomes]
rs4858496	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4858497	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4858500	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4858501	0.90[ASN][1000 genomes]
rs4858502	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4858504	0.81[ASN][1000 genomes]
rs4858506	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4858508	0.86[ASN][1000 genomes]
rs59429714	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6550746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6550748	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6550755	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs6550756	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6767599	0.82[JPT][hapmap]
rs6769173	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6780723	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6780787	0.81[JPT][hapmap]
rs6784195	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6784771	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795492	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796840	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6804123	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6805889	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs716457	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7429470	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7622784	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631334	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7645209	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs778459	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs778460	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs778462	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs778468	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs778470	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs778471	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs778476	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs778480	0.95[JPT][hapmap]
rs778486	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs778494	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs778501	0.81[JPT][hapmap]
rs778506	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs778508	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs778523	0.95[JPT][hapmap]
rs9310715	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809176	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816895	0.86[ASN][1000 genomes]
rs9821101	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9822422	0.91[ASN][1000 genomes]
rs9825778	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9826089	0.83[ASN][1000 genomes]
rs9826647	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9826877	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836787	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9839738	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9841123	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9841944	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846398	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9847027	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9847958	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9848077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849176	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9853489	0.83[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs9854148	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9854590	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859515	0.86[ASN][1000 genomes]
rs9859651	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9861803	0.92[ASN][1000 genomes]
rs9864908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9865602	0.85[ASN][1000 genomes]
rs9873317	0.88[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9874082	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9874519	0.82[ASN][1000 genomes]
rs9874822	0.90[ASN][1000 genomes]
rs9881332	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23292800-23306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:23297000-23307000	Weak transcription	Primary B cells from cord blood	blood
4	chr3:23298400-23305200	Weak transcription	HSMM	muscle
5	chr3:23298800-23311000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:23298800-23336600	Weak transcription	Thymus	Thymus
7	chr3:23299000-23306800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:23299000-23314200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:23300000-23305400	Weak transcription	A549	lung
10	chr3:23300200-23305000	Weak transcription	NH-A	brain
11	chr3:23302400-23305600	Weak transcription	HSMMtube	muscle
12	chr3:23302400-23305800	Weak transcription	Psoas Muscle	Psoas
13	chr3:23302400-23312800	Weak transcription	Lung	lung
14	chr3:23302400-23321000	Weak transcription	Pancreas	Pancrea
15	chr3:23303800-23306800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:23303800-23307200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:23304200-23304600	Weak transcription	Fetal Lung	lung
18	chr3:23304200-23305200	Enhancers	Brain Hippocampus Middle	brain
19	chr3:23304200-23305600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:23304200-23306200	Enhancers	HUVEC	blood vessel
21	chr3:23304200-23306600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:23304200-23307200	Enhancers	Osteobl	bone
23	chr3:23304400-23304600	Enhancers	Right Ventricle	heart
24	chr3:23304400-23304800	Enhancers	NHLF	lung
25	chr3:23304400-23305000	Enhancers	Brain Substantia Nigra	brain
26	chr3:23304400-23306800	Enhancers	NHEK	skin
27	chr3:23304400-23307000	Enhancers	HMEC	breast
28	chr3:23304400-23307200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:23304400-23307200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:23304400-23307200	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links