Variant report

Variant	rs5960093
Chromosome Location	chrX:55744285-55744286
allele	C/G
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:55743951-55744576	MCF-7	breast:	n/a	n/a
2	CTCF	chrX:55744284-55744311	LNCaP	prostate:	n/a	n/a
3	MAX	chrX:55743906-55744310	H1-hESC	embryonic stem cell:	n/a	chrX:55744063-55744076 chrX:55744185-55744200 chrX:55744065-55744074 chrX:55744182-55744201 chrX:55744155-55744164 chrX:55744155-55744164 chrX:55744063-55744076 chrX:55744155-55744164
4	EP300	chrX:55744012-55744524	GM12878	blood:	n/a	n/a
5	RAD21	chrX:55743918-55744958	IMR90	lung:	n/a	n/a
6	CTCF	chrX:55744156-55744363	ProgFib	skin:	n/a	chrX:55744270-55744283
7	TAF1	chrX:55744095-55744337	HepG2	liver:	n/a	n/a
8	CHD1	chrX:55743772-55745165	GM12878	blood:	n/a	n/a
9	POLR2A	chrX:55743863-55744560	ProgFib	skin:	n/a	n/a
10	ZEB1	chrX:55743902-55744749	GM12878	blood:	n/a	n/a
11	POLR2A	chrX:55743768-55744819	Hela-S3	cervix:	n/a	n/a
12	FOS	chrX:55743902-55744312	MCF10A-Er-Src	breast:	n/a	chrX:55743917-55743929
13	ELK1	chrX:55743757-55745142	Hela-S3	cervix:	n/a	n/a
14	CHD2	chrX:55744022-55745006	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD2	chrX:55744017-55744349	K562	blood:	n/a	n/a
16	POLR2A	chrX:55743570-55744577	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chrX:55743744-55745106	GM18505	blood:	n/a	n/a
18	SIN3AK20	chrX:55744001-55744400	K562	blood:	n/a	n/a
19	CREB1	chrX:55743939-55744356	A549	lung:	n/a	n/a
20	TBL1XR1	chrX:55743997-55745031	GM12878	blood:	n/a	n/a
21	POLR2A	chrX:55743877-55744523	HepG2	liver:	n/a	n/a
22	POLR2A	chrX:55743986-55744409	K562	blood:	n/a	n/a
23	POLR2A	chrX:55743882-55744741	PFSK-1	brain:	n/a	n/a
24	MAX	chrX:55743800-55744414	SK-N-SH	brain:	n/a	chrX:55744063-55744076 chrX:55744185-55744200 chrX:55744065-55744074 chrX:55744182-55744201 chrX:55744155-55744164 chrX:55744155-55744164 chrX:55744063-55744076 chrX:55744155-55744164
25	USF1	chrX:55743850-55744670	ECC-1	luminal epithelium:	n/a	chrX:55744149-55744170 chrX:55744155-55744164 chrX:55744153-55744166 chrX:55744155-55744164 chrX:55744156-55744165 chrX:55744186-55744197 chrX:55744154-55744163 chrX:55744153-55744164
26	MXI1	chrX:55743767-55745017	Hela-S3	cervix:	n/a	chrX:55744188-55744197
27	CTCF	chrX:55744176-55745049	IMR90	lung:	n/a	chrX:55744270-55744283
28	MAX	chrX:55743921-55744435	MCF-7	breast:	n/a	chrX:55744063-55744076 chrX:55744185-55744200 chrX:55744065-55744074 chrX:55744182-55744201 chrX:55744155-55744164 chrX:55744155-55744164 chrX:55744063-55744076 chrX:55744155-55744164
29	TAF1	chrX:55744042-55744357	H1-hESC	embryonic stem cell:	n/a	n/a
30	USF1	chrX:55743854-55744614	H1-hESC	embryonic stem cell:	n/a	chrX:55744149-55744170 chrX:55744155-55744164 chrX:55744153-55744166 chrX:55744155-55744164 chrX:55744156-55744165 chrX:55744186-55744197 chrX:55744154-55744163 chrX:55744153-55744164
31	USF1	chrX:55743920-55744332	H1-hESC	embryonic stem cell:	n/a	chrX:55744149-55744170 chrX:55744155-55744164 chrX:55744153-55744166 chrX:55744155-55744164 chrX:55744156-55744165 chrX:55744186-55744197 chrX:55744154-55744163 chrX:55744153-55744164
32	CTCF	chrX:55744275-55744382	MCF-7	breast:	n/a	n/a
33	RCOR1	chrX:55743476-55745276	Hela-S3	cervix:	n/a	n/a
34	SMC3	chrX:55743682-55745220	Hela-S3	cervix:	n/a	chrX:55745066-55745074
35	USF2	chrX:55743885-55744409	HepG2	liver:	n/a	chrX:55744149-55744170 chrX:55744155-55744164 chrX:55744153-55744166 chrX:55744153-55744164 chrX:55744155-55744164 chrX:55744156-55744165 chrX:55744154-55744163
36	POLR2A	chrX:55743775-55744407	PANC-1	pancreas:	n/a	n/a
37	SP1	chrX:55743825-55744294	GM12878	blood:	n/a	chrX:55744043-55744054 chrX:55743979-55743991 chrX:55743979-55743990 chrX:55744045-55744054 chrX:55744043-55744055 chrX:55744043-55744055
38	MAX	chrX:55743859-55744991	Hela-S3	cervix:	n/a	chrX:55744063-55744076 chrX:55744185-55744200 chrX:55744065-55744074 chrX:55744182-55744201 chrX:55744155-55744164 chrX:55744155-55744164 chrX:55744063-55744076 chrX:55744155-55744164
39	TAF1	chrX:55744047-55744389	HepG2	liver:	n/a	n/a
40	POLR2A	chrX:55744100-55744634	GM12891	blood:	n/a	n/a
41	CTCF	chrX:55744250-55744366	Hela-S3	cervix:	n/a	chrX:55744270-55744283
42	TAF1	chrX:55743809-55744588	Hela-S3	cervix:	n/a	n/a
43	SIN3A	chrX:55743914-55745210	H1-hESC	embryonic stem cell:	n/a	chrX:55744186-55744195 chrX:55744154-55744163 chrX:55744188-55744197 chrX:55744064-55744073 chrX:55744099-55744108
44	REST	chrX:55744031-55744342	HepG2	liver:	n/a	n/a
45	TAF1	chrX:55743962-55744483	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chrX:55743893-55744360	K562	blood:	n/a	chrX:55744063-55744076 chrX:55744185-55744200 chrX:55744065-55744074 chrX:55744182-55744201 chrX:55744155-55744164 chrX:55744155-55744164 chrX:55744063-55744076 chrX:55744155-55744164
47	NFYB	chrX:55743766-55744296	GM12878	blood:	n/a	n/a
48	RCOR1	chrX:55743830-55744545	GM12878	blood:	n/a	n/a
49	POLR2A	chrX:55744011-55744446	GM12878	blood:	n/a	n/a
50	POLR2A	chrX:55743984-55744434	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:55744275-55744325	HMEC	breast:	n/a
2	chrX:55744275-55744325	LNCaP	prostate:	n/a
3	chrX:55744275-55744325	GM06990	blood:	n/a
4	chrX:55744275-55744325	AG04450	lung:	fetal
5	chrX:55744275-55744325	HEEpiC	esophagus:	n/a
6	chrX:55744275-55744325	ProgFib	skin:	n/a
7	chrX:55744275-55744325	HRPEpiC	eye:	n/a
8	chrX:55744275-55744325	IMR90	lung:	fetal
9	chrX:55744275-55744325	AG09319	gingival:	n/a
10	chrX:55744275-55744325	HEK293	kidney:	embryo
11	chrX:55744275-55744325	HCPEpiC	choroid plexus:	n/a
12	chrX:55744275-55744325	HUVEC	blood vessel:	n/a
13	chrX:55744275-55744325	NHDF-neo	bronchial:	n/a
14	chrX:55744275-55744325	SK-N-SH	brain:	n/a
15	chrX:55744275-55744325	Hela-S3	cervix:	n/a
16	chrX:55744275-55744325	NHBE	bronchial:	n/a
17	chrX:55744275-55744325	Jurkat	blood:	n/a
18	chrX:55744275-55744325	Caco-2	colon:	n/a
19	chrX:55744275-55744325	SAEC	small airway:	n/a
20	chrX:55744275-55744325	HRE	kidney:	n/a
21	chrX:55744275-55744325	ovcar-3	ovarian:	n/a
22	chrX:55744275-55744325	HAEpiC	amniotic membrane:	n/a
23	chrX:55744275-55744325	HNPCEpiC	eye:	n/a
24	chrX:55744275-55744325	GM12878	blood:	n/a
25	chrX:55744275-55744325	BJ	skin:	n/a
26	chrX:55744275-55744325	HIPEpiC	eye:	n/a
27	chrX:55744275-55744325	Hepatocyte	liver:	n/a
28	chrX:55744275-55744325	NH-A	brain:	n/a
29	chrX:55744275-55744325	U87	brain:	n/a
30	chrX:55744275-55744325	HL-60	blood:	n/a
31	chrX:55744275-55744325	H1-hESC	embryonic stem cell:	embryo
32	chrX:55744275-55744325	AoSMC	blood vessel:	n/a
33	chrX:55744275-55744325	SKMC	muscle:	n/a
34	chrX:55744275-55744325	CMK	blood:	n/a
35	chrX:55744275-55744325	AG10803	skin:	n/a
36	chrX:55744275-55744325	PFSK-1	brain:	n/a
37	chrX:55744275-55744325	HCF	heart:	n/a
38	chrX:55744275-55744325	HCM	heart:	n/a
39	chrX:55744275-55744325	PANC-1	pancreas:	n/a
40	chrX:55744275-55744325	AG04449	skin:	fetal
41	chrX:55744275-55744325	PrEC	prostate:	n/a
42	chrX:55744275-55744325	K562	blood:	n/a
43	chrX:55744275-55744325	AG09309	skin:	n/a
44	chrX:55744275-55744325	RPTEC	kidney:	n/a
45	chrX:55744275-55744325	ECC-1	luminal epithelium:	n/a
46	chrX:55744275-55744325	SK-N-MC	brain:	n/a
47	chrX:55744275-55744325	MCF-7	breast:	n/a
48	chrX:55744275-55744325	A549	lung:	n/a
49	chrX:55744275-55744325	NB4	blood:	n/a
50	chrX:55744275-55744325	GM12892	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chrX:55743259..55745403-chrX:56589658..56591573,2	MCF-7	breast:
2	chrX:55478272..55480275-chrX:55742945..55745674,2	MCF-7	breast:
3	chr1:220267309..220268289-chrX:55744121..55744662,2	Hela-S3	cervix:
4	chrX:55515441..55517417-chrX:55743446..55745792,2	MCF-7	breast:
5	chrX:55744136..55745947-chrX:55757019..55759912,2	MCF-7	breast:
6	chrX:40594651..40595260-chrX:55744181..55744697,2	Hela-S3	cervix:

Variant related genes	Relation type
RRAGB	TF binding region
RRAGB	CpG island
ENSG00000180182	Chromatin interaction
ENSG00000187601	Chromatin interaction
ENSG00000247746	Chromatin interaction
ENSG00000083750	Chromatin interaction
ENSG00000067704	Chromatin interaction
ENSG00000188021	Chromatin interaction
ENSG00000234636	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1007153	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12557467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1325572	1.00[YRI][hapmap]
rs1325573	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1473760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1473761	1.00[YRI][hapmap]
rs17277280	1.00[CEU][hapmap]
rs1927597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2375466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826281	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826283	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826287	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4826413	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5000659	1.00[CEU][hapmap]
rs5913857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5913859	1.00[YRI][hapmap]
rs5914428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5914432	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5914434	1.00[YRI][hapmap]
rs5914436	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5914440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5960480	1.00[YRI][hapmap]
rs6611431	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6612359	1.00[YRI][hapmap]
rs6612417	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs913440	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55743400-55744400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chrX:55743400-55745000	Active TSS	Duodenum Mucosa	Duodenum
3	chrX:55743400-55745000	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chrX:55743400-55745200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chrX:55743400-55745200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chrX:55743400-55745200	Active TSS	Pancreas	Pancrea
7	chrX:55743400-55745400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chrX:55743400-55745400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chrX:55743400-55745400	Active TSS	Brain Cingulate Gyrus	brain
10	chrX:55743400-55745400	Active TSS	Brain Hippocampus Middle	brain
11	chrX:55743400-55745400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chrX:55743400-55745600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chrX:55743400-55745600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chrX:55743400-55745600	Active TSS	A549	lung
15	chrX:55743400-55745800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chrX:55743600-55744800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
17	chrX:55743600-55744800	Active TSS	Primary T cells from cord blood	blood
18	chrX:55743600-55744800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chrX:55743600-55744800	Active TSS	Brain Angular Gyrus	brain
20	chrX:55743600-55744800	Active TSS	Fetal Muscle Leg	muscle
21	chrX:55743600-55744800	Active TSS	HSMM	muscle
22	chrX:55743600-55744800	Active TSS	HUVEC	blood vessel
23	chrX:55743600-55745000	Active TSS	Brain Anterior Caudate	brain
24	chrX:55743600-55745000	Active TSS	Brain Substantia Nigra	brain
25	chrX:55743600-55745000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chrX:55743600-55745000	Active TSS	Fetal Lung	lung
27	chrX:55743600-55745000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chrX:55743600-55745000	Active TSS	Osteobl	bone
29	chrX:55743600-55745200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chrX:55743600-55745200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chrX:55743600-55745200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chrX:55743600-55745200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chrX:55743600-55745200	Active TSS	Muscle Satellite Cultured Cells	--
34	chrX:55743600-55745200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chrX:55743600-55745200	Active TSS	Ovary	ovary
36	chrX:55743600-55745200	Active TSS	Rectal Smooth Muscle	rectum
37	chrX:55743600-55745200	Active TSS	NHLF	lung
38	chrX:55743600-55745400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chrX:55743600-55745400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chrX:55743600-55745400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chrX:55743600-55745400	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chrX:55743600-55745400	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chrX:55743600-55745400	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chrX:55743600-55745400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chrX:55743600-55745400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chrX:55743600-55745400	Active TSS	Fetal Intestine Large	intestine
47	chrX:55743600-55745400	Active TSS	Fetal Intestine Small	intestine
48	chrX:55743600-55745400	Active TSS	Fetal Kidney	kidney
49	chrX:55743600-55745400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chrX:55743600-55745400	Active TSS	Psoas Muscle	Psoas

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