Variant report

Variant	rs5985439
Chromosome Location	chrX:109296696-109296697
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	chrX:109194992..109195876-chrX:109296455..109297524,5	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11152597	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11797230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12841904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1418393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1623948	1.00[JPT][hapmap]
rs1770343	1.00[JPT][hapmap]
rs1774690	1.00[JPT][hapmap]
rs2066364	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs2795994	1.00[JPT][hapmap]
rs2881449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs34247395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4081383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4421522	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs4628434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4893450	0.88[CHB][hapmap]
rs5942620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5942626	0.88[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap]
rs5942628	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs5942629	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs5942880	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5942883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5942886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs5942887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5942890	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs5942896	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs5942897	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs5985271	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5985440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs5985442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs5985446	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs946820	1.00[JPT][hapmap]
rs946821	1.00[JPT][hapmap]
rs946822	1.00[JPT][hapmap]
rs947592	0.88[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531154	chrX:108934095-109332109	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	130 gene(s)	inside rSNPs	diseases
2	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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109247400-109318200	Weak transcription	Thymus	Thymus
2	chrX:109248600-109310200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chrX:109266600-109318000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chrX:109267200-109377800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chrX:109270200-109311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chrX:109273200-109310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chrX:109280200-109331800	Weak transcription	Primary B cells from cord blood	blood
8	chrX:109280400-109316600	Weak transcription	Primary B cells from peripheral blood	blood
9	chrX:109280600-109304600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chrX:109280600-109310200	Weak transcription	Duodenum Mucosa	Duodenum
11	chrX:109282000-109297800	Weak transcription	Fetal Intestine Large	intestine
12	chrX:109282000-109297800	Weak transcription	Gastric	stomach
13	chrX:109282800-109304600	Weak transcription	Brain Hippocampus Middle	brain
14	chrX:109284000-109318200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chrX:109286400-109304000	Weak transcription	Hela-S3	cervix
16	chrX:109286800-109316600	Weak transcription	Primary hematopoietic stem cells	blood
17	chrX:109287600-109297000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chrX:109288600-109312800	Weak transcription	Fetal Intestine Small	intestine
19	chrX:109289200-109325000	Weak transcription	Psoas Muscle	Psoas
20	chrX:109290000-109298600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chrX:109291000-109319400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chrX:109291400-109298000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chrX:109291400-109304400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chrX:109291600-109297800	Weak transcription	Brain Angular Gyrus	brain
25	chrX:109291800-109310800	Weak transcription	Right Ventricle	heart
26	chrX:109293000-109304600	Weak transcription	HSMMtube	muscle
27	chrX:109293200-109306000	Weak transcription	Pancreas	Pancrea
28	chrX:109293400-109304000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chrX:109293600-109304200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chrX:109294000-109303400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chrX:109294000-109316200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chrX:109294200-109315400	Weak transcription	Dnd41	blood
33	chrX:109294800-109297400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chrX:109294800-109297600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chrX:109294800-109298800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chrX:109294800-109299800	Weak transcription	GM12878-XiMat	blood
37	chrX:109295000-109297000	Weak transcription	Ovary	ovary
38	chrX:109295200-109296800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chrX:109295200-109304200	Weak transcription	HSMM	muscle
40	chrX:109295200-109309400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chrX:109295600-109297200	Enhancers	Adipose Nuclei	Adipose
42	chrX:109295600-109298000	Weak transcription	Stomach Smooth Muscle	stomach
43	chrX:109295600-109298600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chrX:109295800-109297000	Weak transcription	Primary T cells from cord blood	blood
45	chrX:109295800-109297000	Weak transcription	A549	lung
46	chrX:109295800-109300000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chrX:109296200-109298400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chrX:109296400-109297400	Strong transcription	K562	blood
49	chrX:109296400-109297800	Strong transcription	Left Ventricle	heart
50	chrX:109296400-109298800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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