Variant report

Variant	rs1415887
Chromosome Location	chrX:138848049-138848050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

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]
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	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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];1.00[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];1.00[MEX][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.86[MEX][hapmap]
rs2491009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2497266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs2497277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][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];1.00[MEX][hapmap]
rs2497284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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];1.00[MEX][hapmap]
rs2805901	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]
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];0.85[MEX][hapmap]
rs4363374	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs4824924	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs5908669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs5908746	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap]
rs5953621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs5953643	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]
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	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][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];0.86[MEX][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]
rs6528650	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]
rs6528651	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]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs6654371	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap]
rs7061584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs7885696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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	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
3	nsv7116	chrX:138815720-138851105	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1415887	ATP11C	cis	lymphoblastoid	seeQTL
rs1415887	STAT1	trans	brain	seeQTL
rs1415887	IFIT3	trans	brain	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138806800-138866800	Weak transcription	Left Ventricle	heart
2	chrX:138807200-138858200	Weak transcription	Primary B cells from cord blood	blood
3	chrX:138814000-138883600	Weak transcription	Gastric	stomach
4	chrX:138814200-138848400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chrX:138815200-138849000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chrX:138815800-138854200	Weak transcription	Thymus	Thymus
7	chrX:138818600-138857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chrX:138819800-138848400	Weak transcription	Fetal Intestine Large	intestine
9	chrX:138821000-138854600	Weak transcription	Ovary	ovary
10	chrX:138821400-138848200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chrX:138821400-138854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chrX:138821400-138870800	Weak transcription	HSMMtube	muscle
13	chrX:138822000-138857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chrX:138822200-138882600	Weak transcription	Osteobl	bone
15	chrX:138822400-138854400	Weak transcription	HSMM	muscle
16	chrX:138824800-138870000	Weak transcription	Colonic Mucosa	Colon
17	chrX:138826000-138854000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chrX:138827000-138895400	Weak transcription	Hela-S3	cervix
19	chrX:138827400-138888800	Weak transcription	Small Intestine	intestine
20	chrX:138828400-138848800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chrX:138829600-138859200	Weak transcription	HepG2	liver
22	chrX:138833000-138848600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chrX:138833000-138849200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chrX:138833000-138907400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chrX:138836000-138848400	Weak transcription	Fetal Thymus	thymus
26	chrX:138836800-138848400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chrX:138837000-138848400	Weak transcription	Fetal Intestine Small	intestine
28	chrX:138837200-138854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chrX:138837400-138848800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chrX:138837400-138849000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chrX:138837400-138853000	Weak transcription	Adipose Nuclei	Adipose
32	chrX:138837400-138855400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chrX:138837800-138848600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chrX:138838000-138848800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chrX:138838200-138850000	Weak transcription	Fetal Muscle Leg	muscle
36	chrX:138838400-138848400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chrX:138838400-138849000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chrX:138838600-138850600	Weak transcription	Primary hematopoietic stem cells	blood
39	chrX:138838600-138852000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chrX:138839000-138849000	Weak transcription	Primary B cells from peripheral blood	blood
41	chrX:138839200-138851800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chrX:138840600-138854200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chrX:138840800-138852600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chrX:138841000-138848400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chrX:138841000-138870000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chrX:138841400-138851400	Weak transcription	HMEC	breast
47	chrX:138841400-138854200	Weak transcription	Fetal Stomach	stomach
48	chrX:138841400-138882600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chrX:138841800-138848200	Weak transcription	Primary T cells from cord blood	blood
50	chrX:138841800-138898600	Weak transcription	HUVEC	blood vessel

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