Variant report

Variant	rs7650079
Chromosome Location	chr3:135764245-135764246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs12630389	0.89[ASN][1000 genomes]
rs12632791	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12633805	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12637541	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059064	0.85[ASN][1000 genomes]
rs13065499	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069408	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072690	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13072782	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13075579	0.94[ASN][1000 genomes]
rs13078865	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13084404	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs13092707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097172	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs13097267	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13100235	0.82[ASN][1000 genomes]
rs1523593	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523599	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1523600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843560	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16843611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140450	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2177407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2400649	0.85[ASN][1000 genomes]
rs34447526	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34683314	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34706807	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35097316	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35209948	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35264626	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35532770	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35946332	0.85[ASN][1000 genomes]
rs35961065	0.90[ASN][1000 genomes]
rs3946444	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4075999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4331626	0.84[ASN][1000 genomes]
rs4678224	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4678288	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4678432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4678434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4678435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55873361	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56152207	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57594457	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60070757	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61791712	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61791714	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439603	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439605	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6439609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6439610	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6439614	0.84[ASN][1000 genomes]
rs6439615	0.85[ASN][1000 genomes]
rs6439618	0.85[ASN][1000 genomes]
rs6439622	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6439623	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6439624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770366	0.81[ASN][1000 genomes]
rs6771950	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6775261	0.85[ASN][1000 genomes]
rs6779903	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6793273	0.84[ASN][1000 genomes]
rs6803786	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7433592	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610302	0.85[ASN][1000 genomes]
rs7625177	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7625607	0.86[ASN][1000 genomes]
rs7635621	0.85[ASN][1000 genomes]
rs9289501	0.82[ASN][1000 genomes]
rs940229	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9682712	0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9758578	0.93[ASN][1000 genomes]
rs9846554	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9852009	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9852169	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9856799	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs9866235	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9868239	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]

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	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:135739800-135767800	Weak transcription	NHDF-Ad	bronchial
4	chr3:135742800-135774200	Weak transcription	HMEC	breast
5	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:135750400-135772800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:135750800-135775800	Weak transcription	Liver	Liver
8	chr3:135753200-135764400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:135753800-135764400	Weak transcription	Fetal Kidney	kidney
10	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:135757400-135765000	Strong transcription	Fetal Stomach	stomach
12	chr3:135758000-135766400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:135758200-135771200	Weak transcription	Stomach Mucosa	stomach
14	chr3:135760800-135767400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:135761200-135767600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:135761600-135764600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:135761600-135766800	Weak transcription	Fetal Brain Male	brain
19	chr3:135761600-135783400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:135762200-135772800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:135762200-135773000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:135762200-135774000	Weak transcription	Brain Angular Gyrus	brain
23	chr3:135762400-135764800	Strong transcription	Brain Hippocampus Middle	brain
24	chr3:135762400-135771400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:135762600-135764800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:135762800-135765600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:135763000-135764400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:135763000-135764600	Strong transcription	Colon Smooth Muscle	Colon
29	chr3:135763000-135765200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:135763000-135765400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:135763000-135765600	Strong transcription	NH-A	brain
32	chr3:135763000-135766400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:135763000-135785600	Weak transcription	Brain Anterior Caudate	brain
34	chr3:135763200-135764400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:135763200-135764600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:135763200-135764600	Strong transcription	Lung	lung
37	chr3:135763200-135764600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:135763200-135764800	Strong transcription	Ovary	ovary
39	chr3:135763200-135764800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr3:135763200-135765000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:135763200-135765000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:135763200-135765000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:135763200-135765000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:135763200-135765000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:135763200-135765000	Strong transcription	Esophagus	oesophagus
46	chr3:135763200-135766000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr3:135763200-135767200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:135763200-135767800	Strong transcription	HSMM	muscle
49	chr3:135763200-135769400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:135763200-135770000	Strong transcription	Fetal Intestine Large	intestine

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