Variant report

Variant	rs2429474
Chromosome Location	chr12:47167074-47167075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1008637	0.82[CEU][hapmap]
rs1073381	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785636	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10785637	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10880988	0.86[ASN][1000 genomes]
rs10880990	0.80[ASN][1000 genomes]
rs10880991	0.80[ASN][1000 genomes]
rs10880993	0.86[ASN][1000 genomes]
rs10880995	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11183565	0.86[ASN][1000 genomes]
rs11183566	0.86[ASN][1000 genomes]
rs11183568	0.80[ASN][1000 genomes]
rs11183570	0.80[ASN][1000 genomes]
rs11183574	0.80[ASN][1000 genomes]
rs11183580	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183584	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183597	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11520328	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12372653	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs180433	0.88[JPT][hapmap]
rs180434	0.88[JPT][hapmap]
rs2080688	0.83[EUR][1000 genomes]
rs2098513	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2408619	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2408620	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2430914	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430918	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465613	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603389	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6582672	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6582674	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7136299	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7305578	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7311780	0.86[ASN][1000 genomes]
rs7975961	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2429474	DBX2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47163400-47167800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr12:47163600-47167400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:47163600-47168400	Enhancers	Hela-S3	cervix
6	chr12:47164200-47187800	Genic enhancers	Liver	Liver
7	chr12:47164600-47167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:47164600-47167400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:47164600-47167800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:47164600-47168400	Enhancers	NHDF-Ad	bronchial
11	chr12:47164600-47168400	Enhancers	NHLF	lung
12	chr12:47164800-47169600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:47165000-47168000	Weak transcription	Fetal Heart	heart
14	chr12:47165000-47169000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:47165200-47169400	Enhancers	Fetal Muscle Leg	muscle
16	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
17	chr12:47165400-47167600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:47165600-47167600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:47165600-47167800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:47165800-47167400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:47165800-47167400	Weak transcription	NH-A	brain
23	chr12:47165800-47168200	Weak transcription	Left Ventricle	heart
24	chr12:47165800-47169600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:47166000-47167400	Genic enhancers	HSMM	muscle
26	chr12:47166000-47167800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:47166000-47168400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:47166000-47169000	Enhancers	HSMMtube	muscle
29	chr12:47166800-47167200	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr12:47166800-47167400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:47166800-47168400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:47166800-47169400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:47167000-47167600	Enhancers	Pancreas	Pancrea
34	chr12:47167000-47167600	Enhancers	Psoas Muscle	Psoas
35	chr12:47167000-47167800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:47167000-47168000	Enhancers	Fetal Brain Male	brain
37	chr12:47167000-47168400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:47167000-47168400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:47167000-47168400	Enhancers	Fetal Lung	lung
40	chr12:47167000-47168400	Enhancers	Osteobl	bone
41	chr12:47167000-47173200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links