Variant report

Variant	rs2805901
Chromosome Location	chrX:138809002-138809003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12687833	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12688014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12688450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12688688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12688705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12689199	1.00[GIH][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1361155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs17281969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17281990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17282067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328647	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs17328703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2183251	1.00[CHB][hapmap]
rs2252290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2485721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2485722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap]
rs2485724	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs2485728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485729	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2491005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2491006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap]
rs2491009	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];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs2497266	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];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2497273	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2497274	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2497277	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2497281	1.00[CHB][hapmap]
rs2497282	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs2497284	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];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2772194	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];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5908669	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];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs5953621	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];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs5953643	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[YRI][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs5953748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5953790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6528650	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];0.95[YRI][hapmap]
rs6528651	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[YRI][hapmap]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap]
rs6654371	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap]
rs7061584	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];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs7885696	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482267	chrX:138669319-138817041	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv532936	chrX:138687855-139384681	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
3	nsv491760	chrX:138780768-139283477	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2805901	STAT1	trans	brain	seeQTL
rs2805901	ATP11C	cis	lymphoblastoid	seeQTL
rs2805901	IFIT3	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138797000-138821000	Weak transcription	Primary T cells from cord blood	blood
2	chrX:138802200-138816200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chrX:138802200-138818800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chrX:138802200-138836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chrX:138802400-138810600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chrX:138802400-138820800	Weak transcription	Hela-S3	cervix
7	chrX:138802400-138821800	Weak transcription	HSMM	muscle
8	chrX:138802600-138810600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chrX:138802600-138820400	Weak transcription	HUVEC	blood vessel
10	chrX:138803400-138810800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chrX:138803800-138815400	Weak transcription	Primary B cells from peripheral blood	blood
12	chrX:138803800-138821000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chrX:138804600-138817000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chrX:138804800-138832000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chrX:138805200-138829200	Weak transcription	Duodenum Mucosa	Duodenum
16	chrX:138805400-138819600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chrX:138805400-138835200	Weak transcription	Primary hematopoietic stem cells	blood
18	chrX:138805600-138815400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chrX:138805800-138820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chrX:138806000-138810600	Weak transcription	Liver	Liver
21	chrX:138806400-138819600	Weak transcription	Fetal Intestine Large	intestine
22	chrX:138806600-138836400	Weak transcription	Dnd41	blood
23	chrX:138806800-138810400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chrX:138806800-138820800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chrX:138806800-138866800	Weak transcription	Left Ventricle	heart
26	chrX:138807200-138858200	Weak transcription	Primary B cells from cord blood	blood
27	chrX:138807400-138817600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chrX:138807600-138820800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chrX:138807600-138831200	Weak transcription	Fetal Muscle Trunk	muscle
30	chrX:138807800-138825400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chrX:138807800-138832400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chrX:138808200-138835600	Weak transcription	Fetal Stomach	stomach
33	chrX:138808400-138818000	Weak transcription	GM12878-XiMat	blood
34	chrX:138808400-138832600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chrX:138809000-138809200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chrX:138809000-138822600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chrX:138809000-138836000	Weak transcription	Adipose Nuclei	Adipose

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