Variant report

Variant	rs17139585
Chromosome Location	chrX:77360724-77360725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chrX:77359135-77361131	NB4	blood:	n/a	n/a
2	MYC	chrX:77360325-77361044	MCF10A-Er-Src	breast:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
3	POLR2A	chrX:77359107-77361001	Hela-S3	cervix:	n/a	n/a
4	MXI1	chrX:77359178-77361136	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chrX:77359212-77360936	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chrX:77359086-77360988	PFSK-1	brain:	n/a	n/a
7	MYC	chrX:77359106-77360907	MCF10A-Er-Src	breast:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
8	POLR2A	chrX:77360419-77360752	HepG2	liver:	n/a	n/a
9	POLR2A	chrX:77360271-77361160	GM12878	blood:	n/a	n/a
10	POLR2A	chrX:77359150-77360768	MCF-7	breast:	n/a	n/a
11	MAZ	chrX:77358574-77360738	IMR90	lung:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
12	CEBPB	chrX:77360299-77360752	K562	blood:	n/a	n/a
13	POLR2A	chrX:77358955-77365614	U87	brain:	n/a	n/a
14	POLR2A	chrX:77360424-77361075	A549	lung:	n/a	n/a
15	POU2F2	chrX:77360363-77360730	GM12878	blood:	n/a	chrX:77360537-77360544 chrX:77360404-77360416 chrX:77360407-77360419
16	WRNIP1	chrX:77360570-77362282	GM12878	blood:	n/a	n/a
17	POLR2A	chrX:77360370-77360749	GM12878	blood:	n/a	n/a
18	CEBPB	chrX:77359144-77361119	Hela-S3	cervix:	n/a	n/a
19	MAX	chrX:77359039-77361121	NB4	blood:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
20	POLR2A	chrX:77359149-77360997	K562	blood:	n/a	n/a
21	MAX	chrX:77360402-77360836	K562	blood:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
22	POLR2A	chrX:77359150-77360954	GM19099	blood:	n/a	n/a
23	MAX	chrX:77360310-77360851	K562	blood:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
24	CEBPB	chrX:77360307-77360742	HepG2	liver:	n/a	n/a
25	POLR2A	chrX:77359144-77360872	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chrX:77358962-77360841	PFSK-1	brain:	n/a	n/a
27	POLR2A	chrX:77358982-77362105	K562	blood:	n/a	n/a
28	MAX	chrX:77360446-77360802	K562	blood:	n/a	chrX:77360539-77360548
29	MAX	chrX:77358932-77360899	A549	lung:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
30	BHLHE40	chrX:77360354-77360888	K562	blood:	n/a	n/a
31	BHLHE40	chrX:77360444-77360891	HepG2	liver:	n/a	n/a
32	SIN3AK20	chrX:77359084-77360939	MCF-7	breast:	n/a	n/a
33	POLR2A	chrX:77359136-77360809	GM12878	blood:	n/a	n/a
34	POLR2A	chrX:77360415-77360774	GM12891	blood:	n/a	n/a
35	POLR2A	chrX:77359091-77361007	K562	blood:	n/a	n/a
36	SIN3A	chrX:77359300-77360746	H1-hESC	embryonic stem cell:	n/a	chrX:77359591-77359600
37	POLR2A	chrX:77360405-77360850	GM12892	blood:	n/a	n/a
38	POLR2A	chrX:77359176-77363971	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chrX:77359099-77362165	U87	brain:	n/a	n/a
40	POLR2A	chrX:77360372-77360741	HepG2	liver:	n/a	n/a
41	POLR2A	chrX:77359122-77360871	K562	blood:	n/a	n/a
42	MYC	chrX:77359028-77360906	K562	blood:	n/a	chrX:77360539-77360548 chrX:77360412-77360422
43	CEBPB	chrX:77360291-77360885	HepG2	liver:	n/a	n/a
44	CHD2	chrX:77359233-77360757	Hela-S3	cervix:	n/a	chrX:77359326-77359333
45	MXI1	chrX:77359161-77360883	HepG2	liver:	n/a	n/a
46	POLR2A	chrX:77358936-77366338	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chrX:77359511-77361271	GM12878	blood:	n/a	n/a
48	POLR2A	chrX:77360612-77360864	HCT-116	colon:	n/a	n/a
49	POLR2A	chrX:77359147-77360905	MCF10A-Er-Src	breast:	n/a	n/a
50	MXI1	chrX:77358632-77361075	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39989213..39989723-chrX:77360277..77361068,2	Hela-S3	cervix:
2	chr14:21852187..21853014-chrX:77360392..77360919,2	Hela-S3	cervix:
3	chrX:48754873..48755476-chrX:77360404..77360974,2	Hela-S3	cervix:
4	chrX:77164605..77167302-chrX:77357779..77361008,3	K562	blood:
5	chrX:77358423..77361508-chrX:77374658..77378510,3	MCF-7	breast:
6	chr6:27114680..27115369-chrX:77360307..77360971,2	Hela-S3	cervix:
7	chr3:73159886..73160621-chrX:77360392..77361319,2	Hela-S3	cervix:

Variant related genes	Relation type
PGK1	TF binding region
ENSG00000259826	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000092201	Chromatin interaction
ENSG00000065883	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000102103	Chromatin interaction
ENSG00000102144	Chromatin interaction
ENSG00000248503	Chromatin interaction
ENSG00000260830	Chromatin interaction
ENSG00000126768	Chromatin interaction
ENSG00000165240	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10521358	0.86[CEU][hapmap]
rs10991	0.82[CHD][hapmap];0.81[MKK][hapmap]
rs167674	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs17139617	0.93[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs2073176	0.81[ASW][hapmap];0.80[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs2073178	0.82[GIH][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap]
rs2227291	0.93[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs2643581	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs320988	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs320990	0.90[ASW][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs320992	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs320995	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs320996	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs321073	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs321074	0.90[ASW][hapmap];0.80[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap]
rs321085	0.80[CEU][hapmap]
rs321086	0.80[CEU][hapmap]
rs321088	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs321090	0.93[GIH][hapmap]
rs4826248	0.90[ASW][hapmap];0.86[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][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	nsv529299	chrX:77040316-77947157	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv532880	chrX:77085352-77769755	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:77358200-77361200	Active TSS	NHEK	skin
2	chrX:77358600-77361000	Active TSS	Rectal Smooth Muscle	rectum
3	chrX:77358600-77361400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chrX:77358600-77363000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chrX:77358800-77360800	Active TSS	HSMM	muscle
6	chrX:77358800-77361000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chrX:77358800-77361000	Active TSS	Colon Smooth Muscle	Colon
8	chrX:77358800-77361200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chrX:77358800-77361200	Active TSS	Brain Hippocampus Middle	brain
10	chrX:77358800-77361400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chrX:77358800-77361600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chrX:77358800-77362000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chrX:77358800-77362000	Active TSS	NHDF-Ad	bronchial
14	chrX:77358800-77362800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chrX:77359000-77360800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chrX:77359000-77360800	Active TSS	Adipose Nuclei	Adipose
17	chrX:77359000-77360800	Active TSS	Brain Anterior Caudate	brain
18	chrX:77359000-77360800	Active TSS	Fetal Kidney	kidney
19	chrX:77359000-77360800	Active TSS	Fetal Lung	lung
20	chrX:77359000-77360800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chrX:77359000-77360800	Active TSS	Rectal Mucosa Donor 31	rectum
22	chrX:77359000-77360800	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chrX:77359000-77360800	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chrX:77359000-77360800	Active TSS	NH-A	brain
25	chrX:77359000-77361000	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chrX:77359000-77361000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chrX:77359000-77361000	Active TSS	Primary T cells from cord blood	blood
28	chrX:77359000-77361000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chrX:77359000-77361000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chrX:77359000-77361000	Active TSS	Brain Cingulate Gyrus	brain
31	chrX:77359000-77361000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chrX:77359000-77361200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chrX:77359000-77361200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chrX:77359000-77361200	Active TSS	Brain Substantia Nigra	brain
35	chrX:77359000-77361200	Active TSS	Fetal Muscle Trunk	muscle
36	chrX:77359000-77361200	Active TSS	Psoas Muscle	Psoas
37	chrX:77359000-77361200	Active TSS	NHLF	lung
38	chrX:77359000-77361400	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chrX:77359000-77361400	Active TSS	Aorta	Aorta
40	chrX:77359000-77361400	Active TSS	Brain Angular Gyrus	brain
41	chrX:77359000-77361400	Active TSS	Fetal Intestine Large	intestine
42	chrX:77359000-77361400	Active TSS	Fetal Intestine Small	intestine
43	chrX:77359000-77361600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chrX:77359000-77361600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chrX:77359000-77361800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chrX:77359000-77361800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chrX:77359000-77361800	Active TSS	Brain Germinal Matrix	brain
48	chrX:77359000-77362000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chrX:77359000-77362000	Active TSS	Colonic Mucosa	Colon
50	chrX:77359000-77362200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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