Variant report

Variant	rs12688450
Chromosome Location	chrX:138873792-138873793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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[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]
rs12688688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12688705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12689199	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1361155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17281969	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]
rs17281990	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]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17282067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17328640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17328647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328703	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]
rs17328709	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][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]
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]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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]
rs2491009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2497266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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]
rs2497277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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]
rs2497284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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]
rs2805901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.84[MEX][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]
rs5908746	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5953621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs5953643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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];0.84[MEX][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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]
rs6528651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs6654371	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs7061584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7885696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12688450	ATP11C	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138814000-138883600	Weak transcription	Gastric	stomach
2	chrX:138822200-138882600	Weak transcription	Osteobl	bone
3	chrX:138827000-138895400	Weak transcription	Hela-S3	cervix
4	chrX:138827400-138888800	Weak transcription	Small Intestine	intestine
5	chrX:138833000-138907400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chrX:138841400-138882600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chrX:138841800-138898600	Weak transcription	HUVEC	blood vessel
8	chrX:138842800-138879600	Weak transcription	Brain Germinal Matrix	brain
9	chrX:138844800-138881400	Weak transcription	Brain Hippocampus Middle	brain
10	chrX:138847600-138875800	Weak transcription	Fetal Kidney	kidney
11	chrX:138847800-138888600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chrX:138847800-138899400	Weak transcription	Aorta	Aorta
13	chrX:138848400-138883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chrX:138848600-138897200	Weak transcription	Brain Anterior Caudate	brain
15	chrX:138849200-138888200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chrX:138849600-138879200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chrX:138849600-138885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chrX:138849600-138898600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chrX:138850200-138885000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chrX:138852600-138890600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chrX:138853000-138908000	Weak transcription	A549	lung
22	chrX:138854400-138876200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chrX:138854800-138908600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chrX:138855000-138915400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chrX:138856200-138907800	Weak transcription	NHDF-Ad	bronchial
26	chrX:138856400-138879400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chrX:138856400-138899800	Weak transcription	K562	blood
28	chrX:138857000-138882600	Weak transcription	Esophagus	oesophagus
29	chrX:138857200-138883800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chrX:138857800-138895000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chrX:138858400-138899800	Weak transcription	Spleen	Spleen
32	chrX:138858600-138876800	Weak transcription	Thymus	Thymus
33	chrX:138859000-138879200	Weak transcription	Primary B cells from cord blood	blood
34	chrX:138859000-138910200	Weak transcription	Fetal Intestine Small	intestine
35	chrX:138861000-138878000	Weak transcription	Lung	lung
36	chrX:138861200-138885000	Weak transcription	Fetal Muscle Trunk	muscle
37	chrX:138863200-138903200	Weak transcription	Ovary	ovary
38	chrX:138864200-138879600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chrX:138865200-138885000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chrX:138865400-138884600	Weak transcription	Brain Angular Gyrus	brain
41	chrX:138865600-138911200	Weak transcription	Rectal Smooth Muscle	rectum
42	chrX:138867000-138883600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chrX:138867400-138885600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chrX:138868000-138883000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chrX:138868200-138883400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chrX:138868200-138913600	Weak transcription	Left Ventricle	heart
47	chrX:138868600-138874600	Weak transcription	Primary hematopoietic stem cells	blood
48	chrX:138868600-138914000	Weak transcription	Stomach Smooth Muscle	stomach
49	chrX:138869000-138879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chrX:138869000-138899200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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