Variant report

Variant	rs12521020
Chromosome Location	chr5:42565843-42565844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10941578	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10941579	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739444	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11740415	1.00[CEU][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11948453	1.00[JPT][hapmap]
rs11949751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955075	1.00[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12516901	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13160458	0.96[CEU][hapmap]
rs13176410	0.90[EUR][1000 genomes]
rs13184352	0.84[CEU][hapmap]
rs28943881	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374598	0.91[EUR][1000 genomes]
rs34466913	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34535288	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34895721	0.85[EUR][1000 genomes]
rs35090794	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4075783	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4242115	1.00[JPT][hapmap]
rs4305645	1.00[JPT][hapmap]
rs4314405	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4365846	0.83[ASW][hapmap];0.96[CEU][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs4368736	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4395642	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[LWK][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4484445	1.00[JPT][hapmap]
rs4489074	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4493680	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4496716	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4504390	0.87[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4533898	0.92[ASN][1000 genomes]
rs4554233	1.00[JPT][hapmap]
rs4866791	1.00[JPT][hapmap]
rs4866936	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs55696942	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61197005	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451626	1.00[JPT][hapmap]
rs6859653	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap]
rs6863381	0.85[CEU][hapmap]
rs6865492	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881929	1.00[CEU][hapmap];0.97[TSI][hapmap]
rs6887718	1.00[JPT][hapmap]
rs6896667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7703713	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7707913	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7712701	0.94[EUR][1000 genomes]
rs7714392	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7721816	1.00[JPT][hapmap]
rs7735889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736209	1.00[CEU][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.92[EUR][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	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	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
4	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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42555400-42566000	Enhancers	Liver	Liver
2	chr5:42562400-42566000	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:42564800-42567000	Enhancers	Fetal Intestine Large	intestine
4	chr5:42564800-42567400	Enhancers	Fetal Heart	heart
5	chr5:42564800-42568200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr5:42565000-42566000	Enhancers	Psoas Muscle	Psoas
7	chr5:42565000-42566200	Enhancers	Left Ventricle	heart
8	chr5:42565000-42566600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:42565000-42566600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr5:42565000-42566800	Enhancers	Fetal Lung	lung
11	chr5:42565000-42567200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr5:42565000-42568000	Enhancers	Fetal Intestine Small	intestine
13	chr5:42565000-42568400	Enhancers	Fetal Muscle Leg	muscle
14	chr5:42565200-42566000	Enhancers	Spleen	Spleen
15	chr5:42565200-42566600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:42565200-42568400	Enhancers	Fetal Stomach	stomach
17	chr5:42565400-42566000	Enhancers	HMEC	breast
18	chr5:42565400-42566400	Weak transcription	Fetal Brain Male	brain
19	chr5:42565400-42566600	Enhancers	Aorta	Aorta
20	chr5:42565400-42566800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:42565400-42568000	Enhancers	Adipose Nuclei	Adipose
22	chr5:42565400-42568800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr5:42565600-42566000	Enhancers	Right Atrium	heart
24	chr5:42565600-42566000	Enhancers	Right Ventricle	heart
25	chr5:42565600-42566200	Enhancers	NHEK	skin
26	chr5:42565600-42567600	Enhancers	Fetal Kidney	kidney
27	chr5:42565600-42568000	Enhancers	Rectal Smooth Muscle	rectum
28	chr5:42565800-42566400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr5:42565800-42566600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:42565800-42566800	Weak transcription	Ovary	ovary
31	chr5:42565800-42566800	Enhancers	Stomach Smooth Muscle	stomach
32	chr5:42565800-42570200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:42565800-42571000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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