Variant report

Variant	rs3939
Chromosome Location	chr10:92672564-92672565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:92670581..92673630-chr10:92677940..92680636,3	MCF-7	breast:
2	chr10:92671333..92674706-chr10:92675096..92677939,3	MCF-7	breast:
3	chr10:92667826..92669650-chr10:92671220..92673051,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10509613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10748555	0.85[CEU][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap]
rs10785975	0.83[JPT][hapmap]
rs10881832	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10881836	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10881847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881849	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186297	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11186300	0.92[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11186342	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186369	0.88[CEU][hapmap];0.92[YRI][hapmap]
rs12261388	0.83[YRI][hapmap]
rs1274446	0.82[EUR][1000 genomes]
rs1274447	0.80[EUR][1000 genomes]
rs1274448	0.81[EUR][1000 genomes]
rs1342085	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1418212	0.85[EUR][1000 genomes]
rs1935347	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1954505	0.80[EUR][1000 genomes]
rs2420367	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs4113478	0.85[EUR][1000 genomes]
rs4471341	0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4522081	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs4933194	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6583735	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6583736	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7073423	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7082558	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7101168	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900386	0.92[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7903572	0.92[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7916848	0.92[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7919103	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9420571	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9420572	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831945	chr10:92590576-92793582	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92646800-92676800	Weak transcription	Right Ventricle	heart
2	chr10:92648400-92684400	Weak transcription	Aorta	Aorta
3	chr10:92648600-92675000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:92648600-92679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:92648600-92681000	Weak transcription	Pancreas	Pancrea
6	chr10:92649200-92675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:92651400-92675000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:92652400-92679400	Weak transcription	Psoas Muscle	Psoas
9	chr10:92654600-92675000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:92654800-92674000	Weak transcription	Fetal Heart	heart
11	chr10:92656400-92678400	Weak transcription	NHDF-Ad	bronchial
12	chr10:92658200-92676800	Weak transcription	NH-A	brain
13	chr10:92661000-92680000	Weak transcription	Placenta	Placenta
14	chr10:92663400-92679600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:92663600-92673400	Weak transcription	Left Ventricle	heart
16	chr10:92665400-92675000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:92665400-92675000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:92665400-92675000	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:92665400-92675200	Weak transcription	Fetal Lung	lung
20	chr10:92665600-92673600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:92666200-92673400	Weak transcription	GM12878-XiMat	blood
22	chr10:92668400-92678600	Enhancers	Dnd41	blood
23	chr10:92671400-92672800	Enhancers	Fetal Thymus	thymus
24	chr10:92671400-92672800	Enhancers	NHEK	skin
25	chr10:92671600-92672600	Enhancers	HepG2	liver
26	chr10:92671600-92672800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr10:92671600-92672800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:92671600-92672800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:92671600-92672800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:92671600-92673000	Enhancers	HMEC	breast
31	chr10:92671600-92674600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:92671800-92672600	Strong transcription	HSMMtube	muscle
33	chr10:92672000-92672600	Genic enhancers	A549	lung
34	chr10:92672200-92672600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:92672200-92672800	Genic enhancers	HSMM	muscle
36	chr10:92672200-92673000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr10:92672200-92673600	Genic enhancers	HUVEC	blood vessel
38	chr10:92672200-92673800	Strong transcription	Osteobl	bone
39	chr10:92672400-92674200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr10:92672400-92674600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr10:92672400-92674800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr10:92672400-92676600	Weak transcription	Hela-S3	cervix
43	chr10:92672400-92679800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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