Variant report

Variant	rs56967490
Chromosome Location	chr15:45742182-45742183
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	FOS	chr15:45742161-45742455	MCF10A-Er-Src	breast:	n/a	chr15:45742340-45742351
2	STAT3	chr15:45741724-45742560	MCF10A-Er-Src	breast:	n/a	chr15:45741791-45741799 chr15:45742377-45742388
3	POLR2A	chr15:45742088-45742726	MCF10A-Er-Src	breast:	n/a	n/a
4	GABPA	chr15:45741989-45742506	MCF-7	breast:	n/a	n/a
5	MYC	chr15:45742144-45742470	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr15:45742047-45742545	MCF10A-Er-Src	breast:	n/a	chr15:45742377-45742388
7	MYC	chr15:45742122-45742595	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr15:45742127-45742527	MCF10A-Er-Src	breast:	n/a	chr15:45742340-45742351
9	MAX	chr15:45741918-45742623	MCF-7	breast:	n/a	n/a
10	FOS	chr15:45742128-45742503	MCF10A-Er-Src	breast:	n/a	chr15:45742340-45742351
11	STAT3	chr15:45742057-45742533	MCF10A-Er-Src	breast:	n/a	chr15:45742377-45742388
12	MYC	chr15:45742148-45742203	MCF-7	breast:	n/a	n/a
13	STAT3	chr15:45742170-45742473	MCF10A-Er-Src	breast:	n/a	chr15:45742377-45742388

No.	Distal block	Cell Line	Cell type
1	chr15:45736069..45742318-chr15:45926037..45929619,6	MCF-7	breast:
2	chr15:45740795..45743926-chr15:45878461..45880935,3	MCF-7	breast:
3	chr15:45693029..45695760-chr15:45741637..45746369,4	MCF-7	breast:

Variant related genes	Relation type
RNU7-5P	TF binding region
ENSG00000259354	TF binding region
ENSG00000104164	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000137767	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10152337	0.96[ASN][1000 genomes]
rs10152697	0.96[ASN][1000 genomes]
rs10851425	0.96[EUR][1000 genomes]
rs12324848	0.96[ASN][1000 genomes]
rs1288852	0.92[EUR][1000 genomes]
rs1288861	0.98[ASN][1000 genomes]
rs1288863	0.96[EUR][1000 genomes]
rs1288865	0.95[EUR][1000 genomes]
rs16942066	0.87[ASN][1000 genomes]
rs1706799	0.85[ASN][1000 genomes]
rs17533716	0.85[ASN][1000 genomes]
rs17535381	0.96[ASN][1000 genomes]
rs17537244	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17618294	0.96[ASN][1000 genomes]
rs2433602	0.98[ASN][1000 genomes]
rs2453518	0.92[EUR][1000 genomes]
rs2453546	0.98[ASN][1000 genomes]
rs2461706	0.98[ASN][1000 genomes]
rs2486287	0.98[ASN][1000 genomes]
rs2668746	0.83[ASN][1000 genomes]
rs55721266	0.96[ASN][1000 genomes]
rs55904415	0.96[ASN][1000 genomes]
rs56267974	0.98[ASN][1000 genomes]
rs56273246	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56306977	0.98[ASN][1000 genomes]
rs56327050	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56937414	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57369693	0.96[ASN][1000 genomes]
rs57419781	0.96[ASN][1000 genomes]
rs61301536	0.98[ASN][1000 genomes]
rs72709081	0.87[ASN][1000 genomes]
rs72709084	0.87[ASN][1000 genomes]
rs72709088	0.96[ASN][1000 genomes]
rs72711253	0.98[ASN][1000 genomes]
rs72711255	0.98[ASN][1000 genomes]
rs72711259	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972405	0.96[ASN][1000 genomes]
rs9972498	0.96[ASN][1000 genomes]
rs9972528	0.96[ASN][1000 genomes]

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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv442701	chr15:45737096-45748752	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	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	chr15:45738200-45746600	Weak transcription	Osteobl	bone
2	chr15:45740400-45743000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr15:45740600-45742200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr15:45740600-45743200	Bivalent Enhancer	HepG2	liver
5	chr15:45740800-45742200	Weak transcription	HMEC	breast
6	chr15:45740800-45742400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:45741000-45742400	Weak transcription	Lung	lung
8	chr15:45741000-45742800	Weak transcription	Small Intestine	intestine
9	chr15:45741000-45743600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:45741000-45746200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:45741000-45746400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:45741200-45743600	Weak transcription	HSMM	muscle
13	chr15:45741400-45742400	Enhancers	Liver	Liver
14	chr15:45741400-45742400	Weak transcription	Gastric	stomach
15	chr15:45741400-45744000	Active TSS	Colonic Mucosa	Colon
16	chr15:45741600-45743600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr15:45741600-45744200	Active TSS	Rectal Smooth Muscle	rectum
18	chr15:45742000-45742200	Enhancers	Pancreas	Pancrea
19	chr15:45742000-45742400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:45742000-45742400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:45742000-45742400	Flanking Active TSS	Hela-S3	cervix
22	chr15:45742000-45742600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:45742000-45742600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr15:45742000-45742600	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr15:45742000-45742800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:45742000-45743200	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr15:45742000-45743600	Active TSS	Stomach Mucosa	stomach
28	chr15:45742000-45744000	Enhancers	Esophagus	oesophagus

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