Variant report

Variant	rs12508739
Chromosome Location	chr4:30947714-30947715
allele	A/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	SP1	chr4:30946983-30947894	HCT-116	colon:	n/a	n/a
2	CBX3	chr4:30947120-30948180	HCT-116	colon:	n/a	chr4:30947943-30947954
3	MAX	chr4:30947104-30947927	HCT-116	colon:	n/a	n/a
4	SIN3AK20	chr4:30947111-30947743	HCT-116	colon:	n/a	n/a
5	SP1	chr4:30947011-30947772	HCT-116	colon:	n/a	n/a
6	CEBPB	chr4:30947001-30947718	HCT-116	colon:	n/a	n/a
7	SRF	chr4:30947066-30947790	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
PCDH7	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12512667	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34067925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35036278	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422383	0.89[TSI][hapmap]
rs4563460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61795878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847748	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7667395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7692684	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7692914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9884332	0.82[EUR][1000 genomes];0.90[ASN][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:28 , 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	chr4:30945400-30950200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:30945400-30954600	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:30946800-30948200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:30947000-30947800	Enhancers	Fetal Intestine Large	intestine
9	chr4:30947000-30948200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:30947200-30947800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:30947200-30947800	Enhancers	NH-A	brain
12	chr4:30947200-30948000	Enhancers	HMEC	breast
13	chr4:30947200-30948200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:30947200-30948200	Enhancers	Fetal Heart	heart
15	chr4:30947200-30948200	Enhancers	Hela-S3	cervix
16	chr4:30947400-30947800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr4:30947400-30947800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:30947400-30948200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:30947400-30948200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:30947400-30948200	Enhancers	Fetal Stomach	stomach
21	chr4:30947400-30948200	Enhancers	Left Ventricle	heart
22	chr4:30947400-30948600	Enhancers	Stomach Mucosa	stomach
23	chr4:30947400-30952200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:30947600-30947800	Enhancers	NHEK	skin
25	chr4:30947600-30948000	Weak transcription	Fetal Intestine Small	intestine
26	chr4:30947600-30948000	Enhancers	HUVEC	blood vessel
27	chr4:30947600-30948200	Enhancers	Aorta	Aorta
28	chr4:30947600-30952600	Weak transcription	Rectal Mucosa Donor 31	rectum

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