Variant report

Variant	rs2027279
Chromosome Location	chrX:80490928-80490929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12389790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1372756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs1372757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1538351	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1954611	0.84[JPT][hapmap]
rs2039717	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs5959087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5959088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5959860	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs6524053	1.00[CEU][hapmap]
rs6616729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2027279	MAPK4	trans	brain	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

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:80460600-80492000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chrX:80465600-80491600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chrX:80468000-80492600	Weak transcription	Primary B cells from peripheral blood	blood
10	chrX:80469400-80497200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chrX:80471600-80491600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chrX:80474600-80500600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chrX:80476000-80496000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chrX:80477800-80496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chrX:80479200-80496200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chrX:80479400-80493000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chrX:80479800-80491800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chrX:80480600-80492400	Weak transcription	GM12878-XiMat	blood
19	chrX:80482400-80497200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chrX:80484800-80492600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chrX:80485000-80493200	Weak transcription	Gastric	stomach
22	chrX:80485200-80493000	Weak transcription	Fetal Stomach	stomach
23	chrX:80485400-80492200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chrX:80485400-80492600	Weak transcription	Duodenum Mucosa	Duodenum
25	chrX:80485400-80492800	Weak transcription	Fetal Intestine Small	intestine
26	chrX:80485400-80496400	Weak transcription	Ovary	ovary
27	chrX:80485600-80492800	Weak transcription	Spleen	Spleen
28	chrX:80485800-80493400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chrX:80486000-80493800	Weak transcription	Brain Angular Gyrus	brain
30	chrX:80486600-80492400	Weak transcription	Dnd41	blood
31	chrX:80486800-80493000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chrX:80486800-80503800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chrX:80487800-80492400	Weak transcription	Primary T cells from cord blood	blood
34	chrX:80488800-80493400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chrX:80489200-80494000	Weak transcription	Colon Smooth Muscle	Colon
36	chrX:80489400-80492800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chrX:80489400-80493000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chrX:80490200-80492200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chrX:80490200-80501400	Weak transcription	Fetal Lung	lung
40	chrX:80490400-80493600	Weak transcription	Primary hematopoietic stem cells	blood
41	chrX:80490400-80493800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chrX:80490600-80492200	Weak transcription	Fetal Intestine Large	intestine
43	chrX:80490600-80492400	Weak transcription	Thymus	Thymus
44	chrX:80490800-80492400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chrX:80490800-80493600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chrX:80490800-80496200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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