Variant report

Variant	rs1288863
Chromosome Location	chr15:45738909-45738910
allele	C/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	POLR2A	chr15:45737319-45739201	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:45738787-45739071	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:45738809-45738983	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45736069..45742318-chr15:45926037..45929619,6	MCF-7	breast:
2	chr15:45692773..45694505-chr15:45738421..45740123,2	MCF-7	breast:
3	chr15:45693986..45696362-chr15:45736299..45740535,4	MCF-7	breast:

Variant related genes	Relation type
RNU7-5P	TF binding region
ENSG00000259354	TF binding region
ENSG00000259342	TF binding region
ENSG00000171763	Chromatin interaction
ENSG00000137767	Chromatin interaction
ENSG00000171766	Chromatin interaction

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];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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];0.84[YRI][hapmap]
rs1288852	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288861	1.00[CHB][hapmap]
rs1288865	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];0.99[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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[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	0.99[EUR][1000 genomes]
rs56327050	0.93[EUR][1000 genomes]
rs56937414	0.99[EUR][1000 genomes]
rs56967490	0.96[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	0.99[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	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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45731400-45740400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:45735200-45740400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:45735200-45740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:45736800-45739200	Enhancers	Placenta	Placenta
5	chr15:45736800-45739200	Enhancers	Gastric	stomach
6	chr15:45737000-45739000	Enhancers	Fetal Intestine Large	intestine
7	chr15:45737000-45739000	Enhancers	Fetal Intestine Small	intestine
8	chr15:45737200-45739000	Enhancers	Liver	Liver
9	chr15:45737200-45739200	Enhancers	Pancreas	Pancrea
10	chr15:45737400-45739000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr15:45737600-45739200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:45738000-45740200	Weak transcription	Small Intestine	intestine
13	chr15:45738200-45739000	Enhancers	Duodenum Mucosa	Duodenum
14	chr15:45738200-45739400	Enhancers	Colonic Mucosa	Colon
15	chr15:45738200-45740200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:45738200-45740200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:45738200-45740200	Weak transcription	A549	lung
18	chr15:45738200-45740200	Weak transcription	HSMMtube	muscle
19	chr15:45738200-45740400	Weak transcription	HMEC	breast
20	chr15:45738200-45746600	Weak transcription	Osteobl	bone
21	chr15:45738400-45739000	Weak transcription	Lung	lung
22	chr15:45738400-45739600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:45738400-45740000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:45738400-45740200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:45738400-45740200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:45738400-45740400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:45738400-45740400	Weak transcription	Spleen	Spleen
28	chr15:45738400-45740400	Weak transcription	GM12878-XiMat	blood
29	chr15:45738400-45740600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr15:45738400-45740600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr15:45738400-45742000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:45738400-45742000	Enhancers	Stomach Mucosa	stomach
33	chr15:45738600-45739000	Weak transcription	Esophagus	oesophagus
34	chr15:45738600-45739000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:45738600-45739200	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links