Variant report

Variant	rs4866790
Chromosome Location	chr5:42500927-42500928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10941577	0.95[ASN][1000 genomes]
rs11738365	0.83[CHB][hapmap]
rs11739243	0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs11741390	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11748084	0.94[ASN][1000 genomes]
rs12514403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515480	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12517368	0.83[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518274	0.83[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12522222	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12522421	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153388	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13166255	0.94[ASN][1000 genomes]
rs13166285	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13169289	0.95[ASN][1000 genomes]
rs13178282	0.94[ASN][1000 genomes]
rs13178652	0.95[ASN][1000 genomes]
rs13189275	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1509455	0.82[CHB][hapmap]
rs1509456	0.82[CHB][hapmap]
rs1509462	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872537	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs16872543	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs16872564	0.83[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1858136	0.83[CHB][hapmap]
rs1960498	0.81[CHB][hapmap]
rs1979994	0.83[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2036745	0.83[CHB][hapmap]
rs2089645	0.84[ASN][1000 genomes]
rs28498583	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28943875	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28943877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs28943879	0.84[ASN][1000 genomes]
rs2940913	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2940917	0.82[CHB][hapmap]
rs2940918	0.82[CHB][hapmap]
rs2940919	0.82[CHB][hapmap]
rs2940937	0.97[ASN][1000 genomes]
rs2940944	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2972392	0.95[ASN][1000 genomes]
rs2972393	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2972407	0.82[CHB][hapmap]
rs2972411	0.82[CHB][hapmap]
rs2972412	0.83[CHB][hapmap]
rs2972413	0.81[CHB][hapmap]
rs2972418	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2972420	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs33956936	0.95[ASN][1000 genomes]
rs34069689	1.00[EUR][1000 genomes]
rs35500216	0.97[ASN][1000 genomes]
rs4130114	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4509029	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4530764	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4866781	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866782	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866785	1.00[EUR][1000 genomes]
rs4866788	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866795	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs4866896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs4866901	0.98[AMR][1000 genomes]
rs4866919	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4866931	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4866932	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866934	0.95[ASN][1000 genomes]
rs4866935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58179197	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451621	0.92[ASN][1000 genomes]
rs6451622	0.87[ASN][1000 genomes]
rs6451624	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6897318	0.95[ASN][1000 genomes]
rs7705834	0.95[ASN][1000 genomes]
rs7710528	0.91[ASN][1000 genomes]
rs7721578	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7723304	0.94[ASN][1000 genomes]
rs949559	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42496000-42501200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr5:42496600-42502200	Enhancers	Liver	Liver
3	chr5:42496800-42503200	Weak transcription	HMEC	breast
4	chr5:42498600-42507600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:42498600-42514800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:42499000-42501000	Enhancers	Adipose Nuclei	Adipose
7	chr5:42499200-42501000	Enhancers	Ovary	ovary
8	chr5:42499200-42503400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:42499400-42501000	Enhancers	Colon Smooth Muscle	Colon
10	chr5:42499400-42501000	Enhancers	Rectal Smooth Muscle	rectum
11	chr5:42500000-42501000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:42500000-42501000	Enhancers	NHEK	skin
13	chr5:42500200-42501200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:42500200-42503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:42500200-42507600	Weak transcription	Spleen	Spleen
16	chr5:42500400-42504400	Weak transcription	Left Ventricle	heart
17	chr5:42500400-42507600	Weak transcription	Psoas Muscle	Psoas
18	chr5:42500400-42507600	Weak transcription	Right Atrium	heart
19	chr5:42500600-42502600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:42500600-42503000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:42500600-42507600	Weak transcription	Aorta	Aorta
22	chr5:42500600-42507600	Weak transcription	Right Ventricle	heart
23	chr5:42500800-42501800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:42500800-42503000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:42500800-42503000	Weak transcription	Fetal Lung	lung
26	chr5:42500800-42503000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:42500800-42507600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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