Variant report

Variant	rs2279587
Chromosome Location	chr5:52214581-52214582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52082232..52084006-chr5:52211443..52214627,3	MCF-7	breast:
2	chr5:52213747..52215537-chr5:52218386..52220869,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248898	Chromatin interaction
ENSG00000213949	Chromatin interaction
ENSG00000152684	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12518145	1.00[YRI][hapmap]
rs12520591	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]
rs12656098	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1445937	1.00[YRI][hapmap]
rs16880493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880627	1.00[YRI][hapmap]
rs2279586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302960	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4145748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60925406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6867926	1.00[YRI][hapmap]
rs7701575	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637769	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52142000-52220200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:52166800-52214800	Weak transcription	Spleen	Spleen
3	chr5:52188800-52218200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:52188800-52228200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:52191600-52218400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:52192200-52218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:52192200-52219600	Weak transcription	Fetal Stomach	stomach
8	chr5:52192200-52220000	Weak transcription	Lung	lung
9	chr5:52193200-52218400	Weak transcription	Fetal Kidney	kidney
10	chr5:52195200-52218400	Weak transcription	Fetal Intestine Large	intestine
11	chr5:52195200-52219000	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:52198400-52218200	Weak transcription	Aorta	Aorta
13	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
14	chr5:52206200-52214800	Weak transcription	Left Ventricle	heart
15	chr5:52206400-52240800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:52211400-52216600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:52211400-52216600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:52211400-52216600	Weak transcription	NHLF	lung
19	chr5:52211400-52216600	Weak transcription	Osteobl	bone
20	chr5:52211400-52218200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:52211400-52218200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:52211400-52218200	Weak transcription	Adipose Nuclei	Adipose
23	chr5:52211400-52218400	Weak transcription	Primary T cells from cord blood	blood
24	chr5:52211400-52220200	Weak transcription	Fetal Intestine Small	intestine
25	chr5:52211400-52221200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:52211400-52239400	Weak transcription	Right Ventricle	heart
27	chr5:52211400-52240200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:52211600-52216600	Weak transcription	NHDF-Ad	bronchial
29	chr5:52211600-52218200	Weak transcription	Fetal Lung	lung
30	chr5:52211600-52218400	Weak transcription	HSMMtube	muscle
31	chr5:52211600-52244400	Weak transcription	HepG2	liver
32	chr5:52211800-52215400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:52211800-52218400	Weak transcription	Dnd41	blood
34	chr5:52212200-52237400	Strong transcription	Liver	Liver
35	chr5:52212800-52225400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:52213000-52218400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:52213200-52214600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:52213200-52217000	Weak transcription	NHEK	skin
39	chr5:52213600-52215200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:52213600-52215400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:52213600-52216400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:52213600-52221400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:52214000-52215200	Strong transcription	Placenta	Placenta
44	chr5:52214400-52215200	Strong transcription	Colon Smooth Muscle	Colon
45	chr5:52214400-52215200	Strong transcription	Rectal Mucosa Donor 29	rectum

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