Variant report

Variant	rs5959857
Chromosome Location	chrX:80492311-80492312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12389790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1372756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1372757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1538351	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1954611	0.84[JPT][hapmap]
rs2027279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2039717	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959860	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6524053	1.00[CEU][hapmap]
rs6616729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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	esv2754822	chrX:80365094-80852865	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:80459200-80492800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chrX:80459400-80503800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chrX:80459600-80492400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chrX:80459600-80496800	Weak transcription	Primary B cells from cord blood	blood
5	chrX:80459600-80497000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chrX:80460000-80493400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chrX:80468000-80492600	Weak transcription	Primary B cells from peripheral blood	blood
8	chrX:80469400-80497200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chrX:80474600-80500600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chrX:80476000-80496000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chrX:80477800-80496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chrX:80479200-80496200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chrX:80479400-80493000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chrX:80480600-80492400	Weak transcription	GM12878-XiMat	blood
15	chrX:80482400-80497200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chrX:80484800-80492600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chrX:80485000-80493200	Weak transcription	Gastric	stomach
18	chrX:80485200-80493000	Weak transcription	Fetal Stomach	stomach
19	chrX:80485400-80492600	Weak transcription	Duodenum Mucosa	Duodenum
20	chrX:80485400-80492800	Weak transcription	Fetal Intestine Small	intestine
21	chrX:80485400-80496400	Weak transcription	Ovary	ovary
22	chrX:80485600-80492800	Weak transcription	Spleen	Spleen
23	chrX:80485800-80493400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chrX:80486000-80493800	Weak transcription	Brain Angular Gyrus	brain
25	chrX:80486600-80492400	Weak transcription	Dnd41	blood
26	chrX:80486800-80493000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chrX:80486800-80503800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chrX:80487800-80492400	Weak transcription	Primary T cells from cord blood	blood
29	chrX:80488800-80493400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chrX:80489200-80494000	Weak transcription	Colon Smooth Muscle	Colon
31	chrX:80489400-80492800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chrX:80489400-80493000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chrX:80490200-80501400	Weak transcription	Fetal Lung	lung
34	chrX:80490400-80493600	Weak transcription	Primary hematopoietic stem cells	blood
35	chrX:80490400-80493800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chrX:80490600-80492400	Weak transcription	Thymus	Thymus
37	chrX:80490800-80492400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chrX:80490800-80493600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chrX:80490800-80496200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chrX:80491000-80496800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chrX:80491200-80492800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chrX:80491200-80493400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chrX:80491200-80493400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chrX:80491200-80493400	Weak transcription	Adipose Nuclei	Adipose
45	chrX:80491200-80494000	Weak transcription	Fetal Thymus	thymus
46	chrX:80491400-80496200	Weak transcription	Lung	lung
47	chrX:80491400-80499200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chrX:80491600-80493400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chrX:80491600-80494000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chrX:80491600-80496400	Strong transcription	Monocytes-CD14+_RO01746	blood

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