Variant report

Variant	rs6788167
Chromosome Location	chr3:23642897-23642898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11129119	0.81[CHB][hapmap]
rs11708160	0.81[CEU][hapmap]
rs11711194	0.86[ASN][1000 genomes]
rs11715841	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs11718082	0.85[ASN][1000 genomes]
rs11916411	0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs11918529	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1498809	0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap]
rs1498811	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs1692617	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs1692622	0.86[GIH][hapmap]
rs1692650	0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap]
rs1692651	0.81[JPT][hapmap]
rs1695200	0.87[CHB][hapmap];0.91[GIH][hapmap]
rs2036226	0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2055310	0.81[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap]
rs2133331	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs2173460	0.81[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2359763	0.81[JPT][hapmap]
rs3104243	0.81[GIH][hapmap];0.81[JPT][hapmap]
rs3111311	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs3817002	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap]
rs4383458	0.84[EUR][1000 genomes]
rs4456808	0.84[EUR][1000 genomes]
rs4484143	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4513393	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4635650	0.83[ASN][1000 genomes]
rs4858518	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57137870	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62256993	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62256994	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6550766	0.81[EUR][1000 genomes]
rs6550767	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6763329	0.80[ASN][1000 genomes]
rs6763535	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6767599	0.94[CHB][hapmap]
rs6770079	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6776424	0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs6780723	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6780787	0.87[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap]
rs6795470	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6797907	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap]
rs6798153	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs6808513	0.87[CHB][hapmap]
rs6810100	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs704533	0.87[CHB][hapmap];0.91[GIH][hapmap]
rs7613091	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs7614146	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7634117	0.83[ASN][1000 genomes]
rs7636826	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7640308	0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7644666	0.85[ASN][1000 genomes]
rs7645209	0.87[CHB][hapmap]
rs7648443	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651893	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778459	0.81[JPT][hapmap]
rs778460	0.81[JPT][hapmap]
rs778462	0.81[JPT][hapmap]
rs778468	0.95[JPT][hapmap]
rs778470	0.81[JPT][hapmap]
rs778471	0.81[JPT][hapmap]
rs778476	0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap]
rs778480	0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs778494	0.95[JPT][hapmap]
rs778499	0.81[CHB][hapmap]
rs778500	0.87[CHB][hapmap]
rs778501	0.87[CHB][hapmap]
rs778510	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs778514	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs778521	0.89[GIH][hapmap];0.91[TSI][hapmap]
rs778523	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9815921	0.82[ASN][1000 genomes]
rs9824359	0.83[ASN][1000 genomes]
rs9830388	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs9856169	0.93[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]

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	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
2	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
3	nsv460479	chr3:23626919-23807550	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv589949	chr3:23626919-23807550	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23606000-23643000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:23628800-23647200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:23631400-23643200	Weak transcription	Left Ventricle	heart
4	chr3:23632800-23643200	Weak transcription	Right Ventricle	heart
5	chr3:23632800-23647200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:23638400-23643200	Weak transcription	Esophagus	oesophagus
7	chr3:23638400-23644400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:23638400-23653000	Weak transcription	Aorta	Aorta
9	chr3:23638400-23653400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:23638800-23653400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:23640600-23643400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:23640600-23643400	Enhancers	Hela-S3	cervix
13	chr3:23640600-23643600	Enhancers	Fetal Muscle Leg	muscle
14	chr3:23640800-23643800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:23640800-23647400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:23641000-23643400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:23641400-23643600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:23641600-23643200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:23641600-23643400	Enhancers	NHDF-Ad	bronchial
20	chr3:23641600-23643400	Enhancers	NHLF	lung
21	chr3:23641600-23644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:23641800-23643400	Enhancers	Ovary	ovary
23	chr3:23641800-23643600	Enhancers	Fetal Stomach	stomach
24	chr3:23641800-23644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:23642000-23643400	Enhancers	Fetal Lung	lung
26	chr3:23642000-23643600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:23642000-23653000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:23642200-23643400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:23642200-23643400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:23642200-23643400	Enhancers	Fetal Brain Male	brain
31	chr3:23642200-23643600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:23642400-23643000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:23642400-23643000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr3:23642400-23643000	Flanking Active TSS	Osteobl	bone
35	chr3:23642400-23643200	Enhancers	Brain Angular Gyrus	brain
36	chr3:23642400-23643400	Enhancers	Brain Anterior Caudate	brain
37	chr3:23642400-23643400	Genic enhancers	HSMM	muscle
38	chr3:23642400-23643400	Enhancers	NH-A	brain
39	chr3:23642400-23643600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr3:23642400-23643600	Enhancers	Fetal Kidney	kidney
41	chr3:23642400-23660800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:23642600-23643000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:23642600-23643200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:23642600-23643200	Enhancers	Brain Germinal Matrix	brain
45	chr3:23642600-23643600	Enhancers	Fetal Heart	heart
46	chr3:23642600-23643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:23642600-23644200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:23642600-23647200	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:23642800-23643000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr3:23642800-23643200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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