Variant report

Variant	rs3817002
Chromosome Location	chr3:23540909-23540910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1027379	0.94[JPT][hapmap]
rs11129116	0.86[JPT][hapmap]
rs11129119	0.87[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11708160	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711072	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11715841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11718082	0.90[ASN][1000 genomes]
rs11916411	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs11918529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12386394	0.83[EUR][1000 genomes]
rs12715048	0.89[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs13064035	0.92[ASN][1000 genomes]
rs13074192	0.90[JPT][hapmap]
rs13087861	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13326048	0.95[JPT][hapmap]
rs1353322	0.89[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1498809	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs1498811	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1692612	0.91[ASN][1000 genomes]
rs1692617	0.84[JPT][hapmap]
rs1692620	0.90[ASN][1000 genomes]
rs1692622	0.81[GIH][hapmap];0.81[YRI][hapmap]
rs1692650	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs1695200	0.94[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs17194786	0.92[ASN][1000 genomes]
rs2036226	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs2055310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2133331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2173460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359759	0.95[JPT][hapmap]
rs3104244	0.86[ASN][1000 genomes]
rs3111311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34080387	0.92[ASN][1000 genomes]
rs4383458	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4456808	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4484143	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4513393	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4635650	0.88[ASN][1000 genomes]
rs4858069	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4858074	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4858496	0.95[JPT][hapmap]
rs4858500	0.95[JPT][hapmap]
rs4858502	0.95[JPT][hapmap]
rs4858505	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858506	0.95[JPT][hapmap]
rs4858509	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55797660	0.83[EUR][1000 genomes]
rs57137870	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58748418	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60430884	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60632986	0.83[EUR][1000 genomes]
rs62256993	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256994	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6550755	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs6550767	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763329	0.95[ASN][1000 genomes]
rs6763535	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs6767599	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6770079	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6770091	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs6775232	0.92[ASN][1000 genomes]
rs6776424	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs6780723	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6780787	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6784195	0.95[JPT][hapmap]
rs6795470	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795968	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6797907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798153	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798328	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805889	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6808513	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs6810100	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704533	0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs716456	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs73043614	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612666	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7614146	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7631334	0.95[JPT][hapmap]
rs7634117	0.92[ASN][1000 genomes]
rs7636826	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7640308	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs7644666	0.90[ASN][1000 genomes]
rs7645209	0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7648443	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651893	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778468	0.95[JPT][hapmap]
rs778475	0.91[ASN][1000 genomes]
rs778476	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs778477	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs778480	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs778482	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778494	0.95[JPT][hapmap]
rs778496	0.89[ASN][1000 genomes]
rs778499	0.88[CHB][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs778500	0.94[CHB][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs778501	0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs778503	0.88[ASN][1000 genomes]
rs778510	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs778514	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs778521	0.89[CEU][hapmap];0.84[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs778523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs778526	0.91[ASN][1000 genomes]
rs952134	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs9815921	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9820922	0.81[EUR][1000 genomes]
rs9821419	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs9824359	0.92[ASN][1000 genomes]
rs9825778	0.95[JPT][hapmap]
rs9830388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9830392	0.89[EUR][1000 genomes]
rs9830742	0.92[ASN][1000 genomes]
rs9836574	0.81[CEU][hapmap];0.81[YRI][hapmap]
rs9839738	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9847958	0.90[JPT][hapmap]
rs9856169	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9859651	0.95[JPT][hapmap]
rs9874082	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23523600-23542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:23526600-23554000	Weak transcription	Primary T cells from cord blood	blood
3	chr3:23528000-23542200	Weak transcription	Right Ventricle	heart
4	chr3:23528600-23542200	Weak transcription	Primary B cells from cord blood	blood
5	chr3:23528600-23552200	Weak transcription	Ovary	ovary
6	chr3:23530600-23542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:23531400-23541600	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:23532200-23547800	Weak transcription	NHLF	lung
9	chr3:23536600-23557200	Weak transcription	Left Ventricle	heart
10	chr3:23537400-23541400	Weak transcription	Psoas Muscle	Psoas
11	chr3:23537400-23542200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:23537400-23542400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:23537400-23542400	Weak transcription	HMEC	breast
14	chr3:23537400-23542600	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:23537400-23542600	Weak transcription	HSMM	muscle
16	chr3:23537400-23542800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:23537400-23543000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:23537400-23551400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:23537400-23559400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:23537600-23542600	Weak transcription	NHEK	skin
21	chr3:23537600-23542800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:23537600-23542800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:23537600-23542800	Weak transcription	Osteobl	bone
24	chr3:23537800-23542200	Weak transcription	Brain Substantia Nigra	brain
25	chr3:23537800-23542600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:23537800-23542800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:23538800-23541600	Weak transcription	Fetal Heart	heart
28	chr3:23539000-23542000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:23539400-23542400	Weak transcription	HSMMtube	muscle
30	chr3:23539600-23550000	Weak transcription	GM12878-XiMat	blood
31	chr3:23540400-23560200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:23540800-23542400	Weak transcription	Aorta	Aorta

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