Variant report

Variant	rs12520591
Chromosome Location	chr5:52229745-52229746
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12518145	1.00[YRI][hapmap]
rs12656098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1445937	1.00[YRI][hapmap]
rs16880493	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16880627	1.00[YRI][hapmap]
rs2279586	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279587	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302960	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4145748	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60925406	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867926	1.00[YRI][hapmap]
rs7701575	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9637769	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3352710	chr5:52227995-52232293	Weak transcription Strong transcription Enhancers Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52206400-52240800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:52211400-52239400	Weak transcription	Right Ventricle	heart
4	chr5:52211400-52240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:52211600-52244400	Weak transcription	HepG2	liver
6	chr5:52212200-52237400	Strong transcription	Liver	Liver
7	chr5:52218600-52237000	Weak transcription	Psoas Muscle	Psoas
8	chr5:52218600-52239400	Weak transcription	Ovary	ovary
9	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
10	chr5:52218800-52240800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:52219000-52230400	Weak transcription	HSMMtube	muscle
12	chr5:52219200-52235200	Weak transcription	NHDF-Ad	bronchial
13	chr5:52219200-52240800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:52219200-52240800	Weak transcription	NHLF	lung
15	chr5:52220000-52243000	Weak transcription	Gastric	stomach
16	chr5:52220400-52239400	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:52220600-52232200	Weak transcription	Spleen	Spleen
18	chr5:52220600-52235600	Weak transcription	Fetal Intestine Small	intestine
19	chr5:52220600-52236600	Weak transcription	Lung	lung
20	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:52221400-52240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:52223800-52231800	Strong transcription	Colon Smooth Muscle	Colon
24	chr5:52224000-52235200	Weak transcription	Fetal Intestine Large	intestine
25	chr5:52224000-52236800	Weak transcription	Aorta	Aorta
26	chr5:52224000-52239400	Weak transcription	Fetal Stomach	stomach
27	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
28	chr5:52225200-52232200	Weak transcription	Left Ventricle	heart
29	chr5:52225200-52239800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:52227000-52240800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:52228400-52232200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:52228400-52235200	Weak transcription	Fetal Lung	lung
33	chr5:52228400-52240800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:52228600-52232200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:52228600-52232200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:52228600-52232200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:52228600-52232400	Weak transcription	Adipose Nuclei	Adipose
38	chr5:52228600-52234600	Weak transcription	Placenta	Placenta
39	chr5:52228600-52235400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:52229200-52232200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:52229200-52236600	Weak transcription	Dnd41	blood
43	chr5:52229600-52232400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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