Variant report

Variant	rs2707975
Chromosome Location	chr3:142611657-142611658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:142611638-142612287	SK-N-SH	brain:	n/a	n/a
2	USF1	chr3:142611654-142611874	H1-hESC	embryonic stem cell:	n/a	n/a
3	PBX3	chr3:142611627-142612074	SK-N-SH	brain:	n/a	n/a
4	USF1	chr3:142611608-142611853	SK-N-SH_RA	brain:	n/a	n/a
5	GATA3	chr3:142611563-142612252	SK-N-SH	brain:	n/a	n/a
6	USF1	chr3:142611597-142611891	HCT-116	colon:	n/a	n/a
7	USF1	chr3:142611528-142611947	K562	blood:	n/a	n/a
8	NFYB	chr3:142611546-142611907	K562	blood:	n/a	n/a
9	NFYB	chr3:142611554-142611832	Hela-S3	cervix:	n/a	n/a
10	USF1	chr3:142611585-142611832	A549	lung:	n/a	n/a
11	USF1	chr3:142611546-142611967	SK-N-SH	brain:	n/a	n/a
12	USF1	chr3:142611597-142611916	SK-N-SH_RA	brain:	n/a	n/a
13	USF2	chr3:142611638-142611921	Hela-S3	cervix:	n/a	chr3:142611753-142611764

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142611367..142612951-chr3:142614638..142616165,2	MCF-7	breast:
2	chr3:142296468..142299283-chr3:142609997..142611852,2	MCF-7	breast:
3	chr3:142609483..142612071-chr3:142616369..142619084,2	K562	blood:
4	chr3:142606798..142610492-chr3:142610655..142614860,4	K562	blood:

No data

Variant related genes	Relation type
PCOLCE2	TF binding region
ENSG00000175054	Chromatin interaction
ENSG00000163710	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1036691	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1457684	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1457685	0.81[EUR][1000 genomes]
rs1463559	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2125125	0.81[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs2581619	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2581620	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2581626	0.82[EUR][1000 genomes]
rs2581629	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2581635	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2581636	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes]
rs2581637	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2608070	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2608075	0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs2608078	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2608079	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2619147	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs2707973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2707977	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2707983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707985	0.87[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs2707991	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2707996	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2707997	0.82[EUR][1000 genomes]
rs4683435	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6778732	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648216	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs893885	0.82[EUR][1000 genomes]
rs9824548	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs984593	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs984594	0.82[CEU][hapmap];0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv437342	chr3:142605233-142622834	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv437343	chr3:142607487-142622834	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3506087	chr3:142609212-142614010	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3506084	chr3:142609712-142613910	Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3506088	chr3:142610248-142612881	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3463561	chr3:142610248-142612883	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3506086	chr3:142610271-142612846	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3506083	chr3:142610303-142612813	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3506082	chr3:142610364-142612765	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3463562	chr3:142610368-142612763	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3506089	chr3:142610368-142612763	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv12862	chr3:142610479-142612181	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv437886	chr3:142610610-142611657	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv520851	chr3:142610610-142611657	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv10332	chr3:142610676-142613653	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142608400-142615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142608600-142615200	Weak transcription	Hela-S3	cervix
3	chr3:142608600-142615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:142608600-142617800	Weak transcription	Aorta	Aorta
5	chr3:142609600-142613400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:142609600-142616800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:142610000-142615200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:142610600-142611800	Enhancers	K562	blood

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