Variant report

Variant	rs2485732
Chromosome Location	chrX:138907986-138907987
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:138906465..138908031-chrX:139012823..139014377,2	MCF-7	breast:
2	chrX:138907383..138910299-chrX:138911001..138913816,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

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]
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];0.86[MEX][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]
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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][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]
rs2485721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap]
rs2485724	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs2485728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2491005	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs2491006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs2491009	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];0.92[MKK][hapmap]
rs2497266	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];0.98[MKK][hapmap]
rs2497273	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2497274	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][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];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2497281	1.00[CHB][hapmap]
rs2497282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap]
rs2497284	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]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2772194	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];0.98[MKK][hapmap]
rs2805901	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]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4239992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4363374	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs4824924	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5908669	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];0.94[MKK][hapmap]
rs5908746	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap]
rs5953621	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];0.85[MKK][hapmap]
rs5953643	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];0.89[MKK][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]
rs5954529	0.92[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];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6528650	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];0.89[MKK][hapmap]
rs6528651	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];0.89[MKK][hapmap]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs6654371	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs7061584	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];0.85[MKK][hapmap]
rs7885696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][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	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2485732	IFIT3	trans	brain	seeQTL
rs2485732	STAT1	trans	brain	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138853000-138908000	Weak transcription	A549	lung
2	chrX:138854800-138908600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chrX:138855000-138915400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chrX:138859000-138910200	Weak transcription	Fetal Intestine Small	intestine
5	chrX:138865600-138911200	Weak transcription	Rectal Smooth Muscle	rectum
6	chrX:138868200-138913600	Weak transcription	Left Ventricle	heart
7	chrX:138868600-138914000	Weak transcription	Stomach Smooth Muscle	stomach
8	chrX:138869000-138915600	Weak transcription	Fetal Stomach	stomach
9	chrX:138870600-138913400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chrX:138880200-138913600	Weak transcription	Primary B cells from cord blood	blood
11	chrX:138881400-138913800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chrX:138884000-138913600	Weak transcription	Fetal Thymus	thymus
13	chrX:138884200-138908200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chrX:138884400-138909200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chrX:138884400-138909600	Weak transcription	Fetal Intestine Large	intestine
16	chrX:138884400-138911200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chrX:138884400-138913600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chrX:138888400-138913000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chrX:138896800-138908000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chrX:138898200-138908000	Weak transcription	HSMMtube	muscle
21	chrX:138899600-138913000	Weak transcription	Primary T cells from cord blood	blood
22	chrX:138899800-138914200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chrX:138900000-138913400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chrX:138900200-138908000	Weak transcription	Fetal Muscle Leg	muscle
25	chrX:138900200-138912800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chrX:138900200-138913000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chrX:138900200-138913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chrX:138900200-138915200	Weak transcription	Brain Germinal Matrix	brain
29	chrX:138900600-138913600	Weak transcription	Primary B cells from peripheral blood	blood
30	chrX:138903600-138913600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chrX:138903800-138908000	Weak transcription	Fetal Heart	heart
32	chrX:138906200-138908600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chrX:138907000-138909200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chrX:138907000-138916800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chrX:138907200-138908000	Enhancers	Stomach Mucosa	stomach
36	chrX:138907200-138908400	Enhancers	H9 Cell Line	embryonic stem cell
37	chrX:138907200-138908600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chrX:138907200-138908600	Enhancers	Brain Angular Gyrus	brain
39	chrX:138907200-138908800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chrX:138907200-138909000	Enhancers	Duodenum Mucosa	Duodenum
41	chrX:138907200-138909200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chrX:138907200-138909200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chrX:138907200-138909400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chrX:138907200-138909400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chrX:138907200-138911800	Enhancers	Osteobl	bone
46	chrX:138907200-138916000	Enhancers	Liver	Liver
47	chrX:138907400-138908200	Enhancers	Brain Hippocampus Middle	brain
48	chrX:138907400-138908200	Strong transcription	K562	blood
49	chrX:138907400-138909000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chrX:138907400-138909200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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