Variant report

Variant	rs4892396
Chromosome Location	chrX:74494470-74494471
allele	G/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:74493428-74494661	K562	blood:	n/a	n/a
2	MYC	chrX:74493239-74494504	K562	blood:	n/a	chrX:74493413-74493422
3	TAF1	chrX:74494348-74494531	SK-N-SH	brain:	n/a	n/a
4	TCF7L2	chrX:74493625-74494739	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chrX:74493627-74494541	Hela-S3	cervix:	n/a	n/a
6	GATA1	chrX:74493178-74495266	PBDE	blood:	n/a	chrX:74495023-74495039 chrX:74493445-74493461 chrX:74493448-74493457 chrX:74493450-74493457 chrX:74493448-74493458 chrX:74493450-74493457 chrX:74495027-74495036 chrX:74495020-74495041 chrX:74493450-74493457 chrX:74495023-74495039 chrX:74493443-74493464
7	BHLHE40	chrX:74493642-74494610	GM12878	blood:	n/a	n/a
8	GABPA	chrX:74493583-74494661	MCF-7	breast:	n/a	chrX:74494524-74494533
9	STAT1	chrX:74493701-74494521	GM12878	blood:	n/a	n/a
10	POLR2A	chrX:74493651-74494625	GM18505	blood:	n/a	n/a
11	ZKSCAN1	chrX:74493719-74494484	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chrX:74494278-74494599	HUVEC	blood vessel:	n/a	n/a
13	CEBPB	chrX:74494290-74494514	IMR90	lung:	n/a	n/a
14	POLR2A	chrX:74493308-74494754	GM12891	blood:	n/a	n/a
15	MAX	chrX:74493793-74494516	K562	blood:	n/a	n/a
16	GABPA	chrX:74494257-74494681	A549	lung:	n/a	chrX:74494524-74494533
17	MAX	chrX:74493760-74494781	NB4	blood:	n/a	n/a
18	MXI1	chrX:74493708-74494555	HepG2	liver:	n/a	n/a
19	PBX3	chrX:74493518-74494622	SK-N-SH	brain:	n/a	chrX:74493852-74493872
20	CEBPB	chrX:74493710-74494592	Hela-S3	cervix:	n/a	n/a
21	MXI1	chrX:74493624-74494964	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chrX:74493583-74494651	GM18951	blood:	n/a	n/a
23	JUND	chrX:74493371-74494555	K562	blood:	n/a	chrX:74493818-74493829 chrX:74493817-74493825 chrX:74493816-74493826 chrX:74493816-74493826
24	TBP	chrX:74493799-74494865	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chrX:74494227-74494544	HUVEC	blood vessel:	n/a	n/a
26	HEY1	chrX:74493911-74494599	K562	blood:	n/a	n/a
27	POLR2A	chrX:74493737-74494712	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chrX:74493667-74494600	Hela-S3	cervix:	n/a	n/a
29	ZNF143	chrX:74493728-74494568	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chrX:74493776-74494612	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chrX:74493802-74494626	K562	blood:	n/a	n/a
32	SMC3	chrX:74493609-74494694	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chrX:74493491-74494716	K562	blood:	n/a	n/a
34	POLR2A	chrX:74493805-74494601	IMR90	lung:	n/a	n/a
35	RAD21	chrX:74493699-74494514	H1-hESC	embryonic stem cell:	n/a	n/a
36	KAP1	chrX:74493453-74494601	U2OS	brain:	n/a	n/a
37	TCF12	chrX:74493484-74494532	A549	lung:	n/a	n/a
38	POLR2A	chrX:74494249-74494697	PFSK-1	brain:	n/a	n/a
39	FOS	chrX:74494326-74494484	MCF10A-Er-Src	breast:	n/a	n/a
40	MTA3	chrX:74493582-74494518	GM12878	blood:	n/a	n/a
41	POLR2A	chrX:74493890-74494693	U87	brain:	n/a	n/a
42	ELK1	chrX:74493689-74494518	Hela-S3	cervix:	n/a	n/a
43	SPI1	chrX:74494373-74494579	K562	blood:	n/a	chrX:74494494-74494507
44	RAD21	chrX:74493719-74494555	Hela-S3	cervix:	n/a	n/a
45	NFYA	chrX:74493442-74494552	Hela-S3	cervix:	n/a	chrX:74493864-74493882
46	IRF1	chrX:74494392-74494556	K562	blood:	n/a	chrX:74494500-74494509 chrX:74494523-74494537
47	TBP	chrX:74493308-74494632	K562	blood:	n/a	n/a
48	MXI1	chrX:74493170-74494774	IMR90	lung:	n/a	chrX:74493407-74493422
49	MXI1	chrX:74493631-74494577	Hela-S3	cervix:	n/a	n/a
50	GTF2F1	chrX:74494374-74494488	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
UPRT	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1017681	1.00[MEX][hapmap]
rs1418343	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap]
rs1936919	1.00[MEX][hapmap]
rs1998492	1.00[MEX][hapmap]
rs2146770	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2181550	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap]
rs2209049	0.89[YRI][hapmap]
rs2209052	1.00[MEX][hapmap]
rs2224753	1.00[MEX][hapmap]
rs2224754	1.00[MEX][hapmap]
rs2367109	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2367177	1.00[MEX][hapmap]
rs4892404	1.00[MEX][hapmap]
rs4892583	1.00[MEX][hapmap];0.86[MKK][hapmap]
rs5937351	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534085	chrX:74360310-74516106	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv13841	chrX:74461978-74657064	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv532360	chrX:74462926-74651249	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1067730	chrX:74463757-74592761	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv532879	chrX:74463757-74592761	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv916109	chrX:74463757-74651249	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 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:74493200-74494800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chrX:74493200-74495000	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chrX:74493200-74495000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chrX:74493200-74495000	Active TSS	Aorta	Aorta
5	chrX:74493200-74495000	Active TSS	Fetal Lung	lung
6	chrX:74493200-74495000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chrX:74493200-74495000	Active TSS	Stomach Smooth Muscle	stomach
8	chrX:74493200-74495200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chrX:74493200-74495200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chrX:74493200-74495200	Active TSS	Brain Anterior Caudate	brain
11	chrX:74493200-74495200	Active TSS	Brain Cingulate Gyrus	brain
12	chrX:74493200-74495200	Active TSS	Rectal Mucosa Donor 31	rectum
13	chrX:74493200-74495200	Active TSS	Rectal Smooth Muscle	rectum
14	chrX:74493200-74495200	Active TSS	HepG2	liver
15	chrX:74493200-74495400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chrX:74493200-74495400	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
17	chrX:74493200-74495800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chrX:74493200-74496000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chrX:74493200-74497400	Active TSS	GM12878-XiMat	blood
20	chrX:74493400-74494600	Active TSS	Primary hematopoietic stem cells	blood
21	chrX:74493400-74494800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chrX:74493400-74494800	Active TSS	Brain Angular Gyrus	brain
23	chrX:74493400-74495000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chrX:74493400-74495000	Active TSS	Primary B cells from cord blood	blood
25	chrX:74493400-74495000	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chrX:74493400-74495000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chrX:74493400-74495000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chrX:74493400-74495000	Active TSS	Brain Substantia Nigra	brain
29	chrX:74493400-74495000	Active TSS	Colonic Mucosa	Colon
30	chrX:74493400-74495000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chrX:74493400-74495000	Active TSS	Fetal Kidney	kidney
32	chrX:74493400-74495000	Active TSS	Placenta	Placenta
33	chrX:74493400-74495000	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chrX:74493400-74495000	Active TSS	Thymus	Thymus
35	chrX:74493400-74495000	Active TSS	HUVEC	blood vessel
36	chrX:74493400-74495000	Active TSS	Monocytes-CD14+_RO01746	blood
37	chrX:74493400-74495200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chrX:74493400-74495200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chrX:74493400-74495200	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chrX:74493400-74495200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chrX:74493400-74495200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chrX:74493400-74495200	Active TSS	Primary T cells fromperipheralblood	blood
43	chrX:74493400-74495200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chrX:74493400-74495200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chrX:74493400-74495200	Active TSS	Liver	Liver
46	chrX:74493400-74495200	Active TSS	Brain Hippocampus Middle	brain
47	chrX:74493400-74495200	Active TSS	Colon Smooth Muscle	Colon
48	chrX:74493400-74495200	Active TSS	Fetal Brain Male	brain
49	chrX:74493400-74495200	Active TSS	A549	lung
50	chrX:74493400-74495200	Active TSS	NHDF-Ad	bronchial

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