Variant report

Variant	rs6844071
Chromosome Location	chr4:30950571-30950572
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	STAT3	chr4:30950203-30950757	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr4:30950277-30950592	MCF-7	breast:	n/a	n/a
3	TCF7L2	chr4:30950087-30950773	Hela-S3	cervix:	n/a	chr4:30950338-30950352 chr4:30950337-30950353 chr4:30950337-30950353 chr4:30950341-30950350
4	POLR2A	chr4:30950297-30950596	HCT-116	colon:	n/a	n/a
5	NFYA	chr4:30950250-30950644	Hela-S3	cervix:	n/a	n/a
6	TCF7L2	chr4:30950084-30950794	HEK293	kidney:	n/a	chr4:30950338-30950352 chr4:30950337-30950353 chr4:30950337-30950353 chr4:30950341-30950350
7	CEBPB	chr4:30950224-30950614	IMR90	lung:	n/a	n/a
8	JUND	chr4:30950095-30950928	HCT-116	colon:	n/a	chr4:30950397-30950409
9	TEAD4	chr4:30950220-30950781	HCT-116	colon:	n/a	n/a
10	USF2	chr4:30950435-30950574	Hela-S3	cervix:	n/a	n/a
11	JUND	chr4:30950173-30950801	HCT-116	colon:	n/a	chr4:30950397-30950409
12	POLR2A	chr4:30950183-30950708	HCT-116	colon:	n/a	n/a
13	KAP1	chr4:30950273-30950751	HEK293	kidney:	n/a	n/a
14	POLR2A	chr4:30950365-30950626	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr4:30950234-30950643	MCF10A-Er-Src	breast:	n/a	n/a
16	TEAD4	chr4:30950243-30950738	HCT-116	colon:	n/a	n/a
17	SIN3AK20	chr4:30950189-30950776	HCT-116	colon:	n/a	n/a
18	STAT3	chr4:30950232-30950736	MCF10A-Er-Src	breast:	n/a	n/a
19	JUN	chr4:30950215-30950780	Hela-S3	cervix:	n/a	chr4:30950397-30950409
20	FOSL1	chr4:30950066-30950766	HCT-116	colon:	n/a	chr4:30950397-30950409
21	TCF7L2	chr4:30950096-30950604	Hela-S3	cervix:	n/a	chr4:30950338-30950352 chr4:30950337-30950353 chr4:30950337-30950353 chr4:30950341-30950350
22	CHD2	chr4:30950232-30950662	Hela-S3	cervix:	n/a	n/a
23	STAT3	chr4:30950324-30950671	MCF10A-Er-Src	breast:	n/a	n/a
24	KAP1	chr4:30950244-30950764	U2OS	brain:	n/a	n/a
25	FOSL1	chr4:30949983-30950846	HCT-116	colon:	n/a	chr4:30950397-30950409
26	RAD21	chr4:30950223-30950889	HCT-116	colon:	n/a	n/a
27	POLR2A	chr4:30950259-30950641	MCF10A-Er-Src	breast:	n/a	n/a
28	SRF	chr4:30950134-30950965	HCT-116	colon:	n/a	n/a
29	STAT3	chr4:30950192-30950747	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr4:30950011-30950804	HCT-116	colon:	n/a	n/a
31	MAX	chr4:30950080-30950789	HCT-116	colon:	n/a	n/a
32	TCF7L2	chr4:30950158-30950709	HCT-116	colon:	n/a	chr4:30950338-30950352 chr4:30950337-30950353 chr4:30950337-30950353 chr4:30950341-30950350
33	JUND	chr4:30950195-30950724	Hela-S3	cervix:	n/a	chr4:30950397-30950409
34	STAT3	chr4:30950240-30950629	MCF10A-Er-Src	breast:	n/a	n/a
35	CBX3	chr4:30950094-30950771	HCT-116	colon:	n/a	chr4:30950155-30950166
36	CEBPB	chr4:30950012-30950922	HCT-116	colon:	n/a	n/a
37	FOS	chr4:30950204-30950773	MCF10A-Er-Src	breast:	n/a	chr4:30950397-30950409
38	SP1	chr4:30949999-30950941	HCT-116	colon:	n/a	n/a
39	FOS	chr4:30950181-30950773	MCF10A-Er-Src	breast:	n/a	chr4:30950397-30950409
40	SP1	chr4:30950014-30950870	HCT-116	colon:	n/a	n/a
41	CBX3	chr4:30950133-30950843	HCT-116	colon:	n/a	chr4:30950155-30950166
42	RCOR1	chr4:30950151-30950629	Hela-S3	cervix:	n/a	n/a
43	FOS	chr4:30950217-30950651	MCF10A-Er-Src	breast:	n/a	chr4:30950397-30950409
44	CEBPB	chr4:30950142-30950762	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr4:30950104-30950798	HCT-116	colon:	n/a	n/a
46	NFYB	chr4:30950259-30950641	Hela-S3	cervix:	n/a	n/a
47	FOS	chr4:30950200-30950666	MCF10A-Er-Src	breast:	n/a	chr4:30950397-30950409
48	RFX5	chr4:30950226-30950722	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr4:30950307-30950667	MCF10A-Er-Src	breast:	n/a	n/a
50	ATF3	chr4:30950197-30950798	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
PCDH7	TF binding region

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10001740	0.84[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10008420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012785	0.83[YRI][hapmap]
rs10027212	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10805301	0.81[AFR][1000 genomes]
rs12642584	0.82[YRI][hapmap]
rs13136231	0.85[CHB][hapmap]
rs4293757	0.81[EUR][1000 genomes]
rs4305479	0.80[EUR][1000 genomes]
rs4466009	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4490422	0.89[YRI][hapmap]
rs4499665	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs4538442	0.89[YRI][hapmap]
rs56190579	0.81[EUR][1000 genomes]
rs61795880	0.81[EUR][1000 genomes]
rs61795883	0.80[EUR][1000 genomes]
rs61795886	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61795889	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6818938	0.89[YRI][hapmap]
rs6822671	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7659873	0.89[YRI][hapmap]
rs7672741	0.91[ASN][1000 genomes]
rs7697578	0.92[ASN][1000 genomes]
rs9992704	0.81[EUR][1000 genomes]
rs9995296	0.81[AFR][1000 genomes]

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	nsv878810	chr4:30823157-30987395	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv998450	chr4:30823631-31628179	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:30928600-30997400	Weak transcription	Fetal Lung	lung
2	chr4:30941600-30951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:30945000-30952400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:30945200-30954000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:30945400-30954600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:30947400-30952200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:30947600-30952600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:30947800-30951600	Weak transcription	Fetal Intestine Large	intestine
9	chr4:30947800-30952000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:30948200-30951600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:30948200-30951800	Weak transcription	Left Ventricle	heart
12	chr4:30948200-30953000	Weak transcription	Aorta	Aorta
13	chr4:30948200-30954200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:30948200-30956000	Weak transcription	Fetal Heart	heart
15	chr4:30949400-30955800	Enhancers	Hela-S3	cervix
16	chr4:30950000-30950600	Enhancers	HUVEC	blood vessel
17	chr4:30950200-30950600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:30950200-30951000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:30950400-30950600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:30950400-30950600	Enhancers	Fetal Stomach	stomach
21	chr4:30950400-30950800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:30950400-30950800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:30950400-30950800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:30950400-30952000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:30950400-30952800	Enhancers	NHEK	skin
26	chr4:30950400-30954800	Enhancers	HMEC	breast

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