Variant report

Variant	rs1288865
Chromosome Location	chr15:45735284-45735285
allele	G/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	CEBPB	chr15:45735087-45735356	IMR90	lung:	n/a	n/a
2	FOS	chr15:45734999-45735350	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr15:45735031-45735326	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr15:45735023-45735333	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr15:45735114-45735322	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr15:45735041-45735350	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr15:45734994-45735350	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr15:45735019-45735339	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr15:45735126-45735325	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr15:45735004-45735339	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr15:45734959-45735390	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000259342	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10152697	1.00[CHB][hapmap]
rs10851425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153829	0.93[JPT][hapmap]
rs1153830	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1153831	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1153832	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1288852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288861	1.00[CHB][hapmap]
rs1288863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16944629	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16952731	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1706799	0.86[CHB][hapmap]
rs17533716	0.86[CHB][hapmap]
rs17535381	1.00[CHB][hapmap]
rs17537244	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs2088164	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2433600	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2453518	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486287	1.00[CHB][hapmap]
rs4448883	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs56273246	0.98[EUR][1000 genomes]
rs56327050	0.94[EUR][1000 genomes]
rs56937414	0.98[EUR][1000 genomes]
rs56967490	0.95[EUR][1000 genomes]
rs6493154	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs6493157	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6493158	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7165838	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7169748	1.00[CEU][hapmap]
rs7170090	1.00[CEU][hapmap]
rs7173983	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs72711259	0.98[EUR][1000 genomes]
rs8023437	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs8025407	1.00[CEU][hapmap]
rs8042811	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9972498	1.00[CHB][hapmap]

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	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45724000-45736800	Weak transcription	Gastric	stomach
2	chr15:45724000-45737200	Weak transcription	Pancreas	Pancrea
3	chr15:45729800-45736600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:45731400-45740400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:45731800-45737000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:45732000-45736800	Weak transcription	A549	lung
7	chr15:45732200-45737000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:45733800-45735400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:45734200-45738000	Enhancers	Stomach Mucosa	stomach
10	chr15:45734800-45735400	Enhancers	Colonic Mucosa	Colon
11	chr15:45735000-45737000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:45735000-45737000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:45735200-45736200	Weak transcription	Placenta	Placenta
14	chr15:45735200-45736200	Weak transcription	Hela-S3	cervix
15	chr15:45735200-45737000	Weak transcription	Fetal Intestine Large	intestine
16	chr15:45735200-45737000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:45735200-45737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:45735200-45737200	Weak transcription	Lung	lung
19	chr15:45735200-45737200	Weak transcription	Osteobl	bone
20	chr15:45735200-45737400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:45735200-45737400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:45735200-45737400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:45735200-45737400	Weak transcription	HSMM	muscle
24	chr15:45735200-45737400	Weak transcription	NHDF-Ad	bronchial
25	chr15:45735200-45737600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:45735200-45737600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:45735200-45737600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:45735200-45740400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:45735200-45740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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