Variant report

Variant	rs2414128
Chromosome Location	chr15:52369728-52369729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10518674	0.80[JPT][hapmap]
rs11070875	0.86[JPT][hapmap]
rs11070876	0.84[EUR][1000 genomes]
rs11070877	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11636443	0.92[CEU][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11637573	0.88[EUR][1000 genomes]
rs12591870	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2414127	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4542605	0.83[ASN][1000 genomes]
rs4627278	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs62015206	0.83[EUR][1000 genomes]
rs6493534	0.85[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7163418	0.95[JPT][hapmap]
rs7166425	0.83[ASN][1000 genomes]
rs8034167	0.95[JPT][hapmap];0.83[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	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1039841	chr15:52357448-52381377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3437569	chr15:52367063-52372248	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2414128	GNB5	cis	multi-tissue	Pritchard
rs2414128	TMOD2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52353200-52370800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:52357200-52371200	Weak transcription	Spleen	Spleen
3	chr15:52357600-52373200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:52357800-52370800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:52358600-52371000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:52362400-52371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:52362800-52374600	Weak transcription	Small Intestine	intestine
8	chr15:52364600-52374000	Weak transcription	Pancreas	Pancrea
9	chr15:52367600-52373200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:52368400-52370600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:52368600-52369800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:52368600-52370000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:52368600-52370800	Enhancers	Liver	Liver
14	chr15:52368600-52371200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:52368600-52371200	Enhancers	HSMM	muscle
16	chr15:52368600-52371400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:52368600-52371400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:52368600-52371800	Enhancers	Fetal Intestine Large	intestine
19	chr15:52368800-52369800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:52368800-52369800	Enhancers	NH-A	brain
21	chr15:52368800-52370000	Enhancers	NHLF	lung
22	chr15:52368800-52370200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:52368800-52371200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:52368800-52371200	Enhancers	Fetal Intestine Small	intestine
25	chr15:52368800-52371200	Enhancers	K562	blood
26	chr15:52368800-52371800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr15:52369000-52369800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:52369000-52369800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr15:52369000-52369800	Enhancers	Hela-S3	cervix
30	chr15:52369000-52369800	Flanking Active TSS	HMEC	breast
31	chr15:52369000-52369800	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr15:52369000-52369800	Flanking Active TSS	NHDF-Ad	bronchial
33	chr15:52369000-52369800	Flanking Active TSS	NHEK	skin
34	chr15:52369000-52370000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:52369000-52371000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:52369000-52371200	Enhancers	Esophagus	oesophagus
37	chr15:52369000-52371400	Enhancers	GM12878-XiMat	blood
38	chr15:52369400-52369800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:52369400-52369800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:52369400-52370800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:52369600-52369800	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr15:52369600-52370000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr15:52369600-52370000	Enhancers	HSMMtube	muscle
44	chr15:52369600-52370000	Enhancers	Osteobl	bone
45	chr15:52369600-52370600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:52369600-52371400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:52369600-52372000	Enhancers	A549	lung
48	chr15:52369600-52373000	Weak transcription	Placenta Amnion	Placenta Amnion

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