Variant report

Variant	rs6647038
Chromosome Location	chrX:73339440-73339441
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:73339231-73339536	Hela-S3	cervix:	n/a	n/a
2	MYC	chrX:73339324-73339563	HUVEC	blood vessel:	n/a	chrX:73339553-73339563
3	MYC	chrX:73339152-73339555	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL1	chrX:73338973-73339630	HCT-116	colon:	n/a	n/a
5	JUN	chrX:73339105-73339540	Hela-S3	cervix:	n/a	n/a
6	FOS	chrX:73339114-73339496	MCF10A-Er-Src	breast:	n/a	chrX:73339294-73339305
7	FOS	chrX:73339116-73339538	HUVEC	blood vessel:	n/a	chrX:73339294-73339305
8	TBP	chrX:73339105-73339531	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chrX:73339106-73339593	Hela-S3	cervix:	n/a	n/a
10	FOS	chrX:73339135-73339469	MCF10A-Er-Src	breast:	n/a	chrX:73339294-73339305
11	GTF2F1	chrX:73339221-73339523	Hela-S3	cervix:	n/a	n/a
12	FOS	chrX:73339104-73339471	MCF10A-Er-Src	breast:	n/a	chrX:73339294-73339305
13	FOSL2	chrX:73339109-73339600	SK-N-SH	brain:	n/a	n/a
14	RAD21	chrX:73339094-73339532	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chrX:73339171-73339662	Hela-S3	cervix:	n/a	n/a
16	FOSL1	chrX:73339081-73339593	HCT-116	colon:	n/a	n/a
17	FOSL2	chrX:73339195-73339511	MCF-7	breast:	n/a	n/a
18	KAP1	chrX:73339012-73339748	U2OS	brain:	n/a	n/a
19	SMARCC1	chrX:73338438-73339508	Hela-S3	cervix:	n/a	n/a
20	MAX	chrX:73338991-73339730	Hela-S3	cervix:	n/a	chrX:73339553-73339563
21	TCF12	chrX:73339281-73339720	SK-N-SH	brain:	n/a	n/a
22	USF2	chrX:73339066-73339570	Hela-S3	cervix:	n/a	n/a
23	MYC	chrX:73339223-73339660	Hela-S3	cervix:	n/a	chrX:73339553-73339563
24	BRCA1	chrX:73339085-73339448	Hela-S3	cervix:	n/a	n/a
25	MAX	chrX:73339126-73339716	HCT-116	colon:	n/a	chrX:73339553-73339563
26	EP300	chrX:73339104-73339611	Hela-S3	cervix:	n/a	n/a
27	TFAP2A	chrX:73337886-73339550	Hela-S3	cervix:	n/a	chrX:73338511-73338526
28	RFX5	chrX:73339205-73339440	Hela-S3	cervix:	n/a	n/a
29	JUND	chrX:73339047-73339562	Hela-S3	cervix:	n/a	n/a
30	MAX	chrX:73338547-73339745	NB4	blood:	n/a	chrX:73339553-73339563
31	FOS	chrX:73339114-73339488	MCF10A-Er-Src	breast:	n/a	chrX:73339294-73339305
32	RCOR1	chrX:73339083-73339452	Hela-S3	cervix:	n/a	n/a
33	SMC3	chrX:73338933-73339487	Hela-S3	cervix:	n/a	n/a
34	CHD2	chrX:73339138-73339560	Hela-S3	cervix:	n/a	n/a
35	MYC	chrX:73339309-73339578	MCF10A-Er-Src	breast:	n/a	chrX:73339553-73339563
36	TFAP2C	chrX:73337965-73339571	Hela-S3	cervix:	n/a	chrX:73338565-73338580
37	MAX	chrX:73339048-73339715	Hela-S3	cervix:	n/a	chrX:73339553-73339563
38	TCF12	chrX:73339053-73339839	SK-N-SH	brain:	n/a	n/a
39	CEBPB	chrX:73339089-73339598	Hela-S3	cervix:	n/a	n/a
40	FOS	chrX:73338955-73339579	Hela-S3	cervix:	n/a	chrX:73339294-73339305
41	FOSL2	chrX:73339124-73339528	A549	lung:	n/a	n/a
42	MYC	chrX:73339005-73339733	NB4	blood:	n/a	chrX:73339553-73339563

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:73335297..73337411-chrX:73337819..73340758,2	MCF-7	breast:

Variant related genes	Relation type
DDX3YP1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1151599	1.00[CHB][hapmap]
rs1151602	1.00[CHB][hapmap]
rs1341326	1.00[CHB][hapmap]
rs174164	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs2066449	1.00[CHB][hapmap]
rs4892491	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs5981258	1.00[CHB][hapmap]
rs5981589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs5981594	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs5981595	0.82[CHB][hapmap]
rs604174	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs6607463	0.80[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs6647445	1.00[CHB][hapmap]
rs6647446	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap]
rs6647448	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6647454	1.00[CHB][hapmap]
rs6655556	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3364045	chrX:72896383-73699363	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	301 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:73306800-73353000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chrX:73319000-73340800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chrX:73319600-73347800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chrX:73320400-73343000	Weak transcription	Left Ventricle	heart
5	chrX:73321600-73349400	Weak transcription	Right Ventricle	heart
6	chrX:73322000-73340800	Weak transcription	Fetal Intestine Large	intestine
7	chrX:73323400-73349400	Weak transcription	Brain Angular Gyrus	brain
8	chrX:73323600-73353000	Weak transcription	Aorta	Aorta
9	chrX:73324400-73351200	Weak transcription	Duodenum Mucosa	Duodenum
10	chrX:73325200-73340800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chrX:73326000-73341000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chrX:73326400-73340800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chrX:73327200-73340800	Weak transcription	Liver	Liver
14	chrX:73331200-73341000	Weak transcription	Brain Germinal Matrix	brain
15	chrX:73334200-73343200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chrX:73334400-73340800	Weak transcription	Ovary	ovary
17	chrX:73336200-73346400	Weak transcription	Rectal Smooth Muscle	rectum
18	chrX:73336600-73340800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chrX:73337600-73339600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chrX:73337600-73339600	Strong transcription	Fetal Intestine Small	intestine
21	chrX:73337600-73339600	Enhancers	Placenta	Placenta
22	chrX:73337800-73339600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chrX:73338000-73339600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chrX:73338000-73349000	Weak transcription	Brain Cingulate Gyrus	brain
25	chrX:73338200-73339600	Enhancers	HMEC	breast
26	chrX:73338200-73340800	Weak transcription	Adipose Nuclei	Adipose
27	chrX:73338400-73339600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chrX:73338400-73339600	Flanking Active TSS	Hela-S3	cervix
29	chrX:73338600-73339600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chrX:73338600-73340000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chrX:73338600-73340000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chrX:73338800-73339600	Enhancers	HSMMtube	muscle
33	chrX:73338800-73339600	Enhancers	NHDF-Ad	bronchial
34	chrX:73338800-73339800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chrX:73338800-73340000	Enhancers	Muscle Satellite Cultured Cells	--
36	chrX:73339000-73339600	Enhancers	NHLF	lung
37	chrX:73339000-73339800	Enhancers	HUVEC	blood vessel
38	chrX:73339000-73340000	Enhancers	NH-A	brain
39	chrX:73339000-73340200	Enhancers	HSMM	muscle
40	chrX:73339000-73349400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chrX:73339200-73339600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chrX:73339200-73339600	Enhancers	A549	lung
43	chrX:73339200-73339600	Enhancers	Osteobl	bone
44	chrX:73339200-73339800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chrX:73339200-73341000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chrX:73339200-73352800	Weak transcription	Primary hematopoietic stem cells	blood
47	chrX:73339400-73339600	Bivalent Enhancer	NHEK	skin
48	chrX:73339400-73339800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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