Variant report

Variant	rs12902461
Chromosome Location	chr15:40556713-40556714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40556498..40560954-chr15:40561713..40567483,5	MCF-7	breast:
2	chr15:40554698..40556971-chr15:40557750..40559311,2	K562	blood:

Variant related genes	Relation type
ENSG00000137843	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1075506	0.97[ASN][1000 genomes]
rs1075507	0.97[ASN][1000 genomes]
rs1075508	0.97[ASN][1000 genomes]
rs2277564	0.85[ASN][1000 genomes]
rs2412504	0.96[ASN][1000 genomes]
rs3743131	0.97[ASN][1000 genomes]
rs3743132	0.96[ASN][1000 genomes]
rs3743135	0.95[ASN][1000 genomes]
rs6492939	0.81[EUR][1000 genomes]
rs6492940	0.81[EUR][1000 genomes]
rs7162809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034871	0.81[EUR][1000 genomes]
rs936217	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv904097	chr15:40555065-40595627	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40546000-40558400	Weak transcription	Brain Anterior Caudate	brain
2	chr15:40546000-40558600	Weak transcription	Brain Angular Gyrus	brain
3	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
4	chr15:40546200-40568200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:40546800-40559200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:40550000-40568000	Weak transcription	Spleen	Spleen
7	chr15:40550400-40566800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:40550800-40558200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:40551200-40558800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:40551400-40558800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:40551400-40561600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:40551400-40571000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:40551600-40557000	Weak transcription	Placenta	Placenta
14	chr15:40551600-40557200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:40551600-40557200	Weak transcription	HMEC	breast
16	chr15:40551600-40557600	Weak transcription	Pancreas	Pancrea
17	chr15:40551600-40558200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:40551600-40558600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:40551600-40560000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:40551600-40561800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr15:40553800-40558400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:40553800-40570400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:40554600-40557600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:40554600-40557800	Strong transcription	NHEK	skin
25	chr15:40554800-40559000	Enhancers	Hela-S3	cervix
26	chr15:40554800-40559200	Weak transcription	Fetal Brain Female	brain
27	chr15:40555000-40557000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr15:40555000-40557600	Weak transcription	A549	lung
29	chr15:40555000-40560600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:40555200-40558600	Strong transcription	Esophagus	oesophagus
31	chr15:40555400-40566600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:40555600-40558000	Weak transcription	Gastric	stomach
33	chr15:40555600-40558800	Weak transcription	HSMMtube	muscle
34	chr15:40555800-40556800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:40555800-40558000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:40555800-40558600	Weak transcription	HSMM	muscle
37	chr15:40555800-40558600	Weak transcription	NH-A	brain
38	chr15:40555800-40558600	Weak transcription	NHDF-Ad	bronchial
39	chr15:40555800-40558800	Weak transcription	Osteobl	bone
40	chr15:40556000-40556800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:40556000-40556800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:40556000-40557400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:40556000-40557400	Enhancers	Ovary	ovary
44	chr15:40556000-40558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:40556000-40558400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:40556000-40558400	Weak transcription	Brain Germinal Matrix	brain
47	chr15:40556000-40558600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:40556000-40558800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:40556000-40558800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:40556200-40558400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links