Variant report

Variant	rs6872806
Chromosome Location	chr5:41336050-41336051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10462017	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10512774	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10512775	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11737958	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11739235	0.96[ASN][1000 genomes]
rs11739338	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11739372	0.96[ASN][1000 genomes]
rs11739553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11739969	0.98[ASN][1000 genomes]
rs11740787	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11741144	0.97[ASN][1000 genomes]
rs11741795	0.94[ASN][1000 genomes]
rs11744499	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11747859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1373639	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1423312	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460953	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs161087	0.81[EUR][1000 genomes]
rs16871219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16871220	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16871222	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16871258	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs16871269	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1822820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1904178	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1904179	0.96[ASN][1000 genomes]
rs2054445	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2161542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2197422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329601	0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs2329602	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2329604	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2329671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2860000	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs318837	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs318839	0.81[EUR][1000 genomes]
rs318842	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs4245978	0.97[ASN][1000 genomes]
rs4957153	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4957389	0.97[ASN][1000 genomes]
rs4957390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4957391	0.97[ASN][1000 genomes]
rs4957392	0.97[ASN][1000 genomes]
rs60271243	0.88[ASN][1000 genomes]
rs60917374	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61282403	0.97[ASN][1000 genomes]
rs67043243	0.98[ASN][1000 genomes]
rs6886372	0.96[ASN][1000 genomes]
rs6886899	0.96[ASN][1000 genomes]
rs6898606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755961	0.96[ASN][1000 genomes]
rs72755967	0.97[ASN][1000 genomes]
rs72755968	0.97[ASN][1000 genomes]
rs72755970	0.97[ASN][1000 genomes]
rs72755972	0.97[ASN][1000 genomes]
rs72755973	0.97[ASN][1000 genomes]
rs72755982	0.94[ASN][1000 genomes]
rs72755983	0.96[ASN][1000 genomes]
rs72755984	0.94[ASN][1000 genomes]
rs73075962	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs765176	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs765177	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7701760	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7703589	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7704046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7723649	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7724627	0.93[ASN][1000 genomes]
rs7725517	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7727658	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs7729454	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7735604	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs978727	0.88[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	nsv427717	chr5:41201377-41369202	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv830269	chr5:41209113-41393536	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1851387	chr5:41336050-41423631	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41333400-41337200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:41333800-41345800	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr5:41334000-41336600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:41334000-41337600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:41334200-41336200	Enhancers	Fetal Heart	heart
6	chr5:41334800-41336200	Weak transcription	Adipose Nuclei	Adipose
7	chr5:41334800-41336200	Enhancers	Brain Cingulate Gyrus	brain
8	chr5:41334800-41336200	Enhancers	Ovary	ovary
9	chr5:41335000-41336800	Enhancers	Brain Substantia Nigra	brain
10	chr5:41335000-41336800	Weak transcription	Right Atrium	heart
11	chr5:41335200-41336800	Enhancers	Brain Anterior Caudate	brain
12	chr5:41335200-41337400	Enhancers	Colon Smooth Muscle	Colon
13	chr5:41335400-41336600	Weak transcription	Left Ventricle	heart
14	chr5:41335400-41336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:41335400-41336800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:41335400-41337400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:41335400-41338200	Weak transcription	Fetal Lung	lung
18	chr5:41335600-41336200	Enhancers	Brain Hippocampus Middle	brain
19	chr5:41335600-41336600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:41335800-41336800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:41335800-41337400	Enhancers	Right Ventricle	heart
22	chr5:41336000-41337000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:41336000-41338200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links