Variant report

Variant	rs5942626
Chromosome Location	chrX:109358807-109358808
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:38495589..38497134-chrX:109357946..109359864,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229589	Chromatin interaction
ENSG00000114739	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11152597	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs11797230	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs12841904	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1418393	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs1623948	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs1770343	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs1774690	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs1774691	0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2066364	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap]
rs2791640	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2795991	0.87[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2795992	0.87[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2795993	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2795994	0.87[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap]
rs2881449	0.88[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap]
rs34247395	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4081383	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs4421522	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs4628434	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs4893450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5942620	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942628	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs5942629	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs5942880	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs5942883	0.88[CHB][hapmap];0.85[GIH][hapmap]
rs5942886	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942887	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942890	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs5942896	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs5942897	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs5985271	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5985439	0.88[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap]
rs5985440	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5985442	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5985446	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs946820	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs946821	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs946822	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs947592	0.85[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3369563	chrX:109079631-109573656	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	142 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109267200-109377800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chrX:109331200-109382400	Weak transcription	Right Ventricle	heart
3	chrX:109331600-109363200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chrX:109333600-109365200	Weak transcription	Primary T cells from cord blood	blood
5	chrX:109334000-109402600	Weak transcription	Primary B cells from cord blood	blood
6	chrX:109338000-109362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chrX:109346800-109366200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chrX:109346800-109378000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chrX:109350200-109368800	Weak transcription	Psoas Muscle	Psoas
10	chrX:109350200-109374600	Weak transcription	Esophagus	oesophagus
11	chrX:109350200-109385200	Weak transcription	Pancreas	Pancrea
12	chrX:109350800-109361200	Weak transcription	Fetal Thymus	thymus
13	chrX:109350800-109364600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chrX:109350800-109371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chrX:109351400-109368400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chrX:109351600-109380200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chrX:109352400-109364800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chrX:109352400-109402400	Weak transcription	Primary B cells from peripheral blood	blood
19	chrX:109352400-109414000	Weak transcription	Dnd41	blood
20	chrX:109352600-109363200	Weak transcription	Adipose Nuclei	Adipose
21	chrX:109353000-109368800	Weak transcription	Left Ventricle	heart
22	chrX:109353000-109375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chrX:109353200-109389000	Weak transcription	Hela-S3	cervix
24	chrX:109354000-109363200	Weak transcription	A549	lung
25	chrX:109354200-109376800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chrX:109354200-109382400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chrX:109355000-109370800	Weak transcription	Ovary	ovary
28	chrX:109355800-109362800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chrX:109356200-109359200	Weak transcription	Fetal Intestine Large	intestine
30	chrX:109356400-109377200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chrX:109356600-109363000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chrX:109356600-109363200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chrX:109356800-109363600	Weak transcription	HSMM	muscle
34	chrX:109357000-109359000	Weak transcription	Fetal Intestine Small	intestine
35	chrX:109357600-109359600	Weak transcription	Duodenum Mucosa	Duodenum
36	chrX:109358000-109382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chrX:109358800-109361800	Weak transcription	K562	blood

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