Variant report

Variant	rs11172898
Chromosome Location	chr12:59464453-59464454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10506357	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877200	0.86[ASN][1000 genomes]
rs10877203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172824	1.00[ASW][hapmap]
rs11172857	1.00[AFR][1000 genomes]
rs11172858	1.00[AFR][1000 genomes]
rs11172861	1.00[AFR][1000 genomes]
rs11172862	1.00[AFR][1000 genomes]
rs11172866	0.86[ASN][1000 genomes]
rs11172867	0.86[ASN][1000 genomes]
rs11172868	1.00[AFR][1000 genomes]
rs11172869	0.86[ASN][1000 genomes]
rs11172870	0.86[ASN][1000 genomes]
rs11172873	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172874	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172876	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172878	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172880	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172881	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172882	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172888	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172891	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12367126	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12368035	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12368658	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12369750	0.86[ASN][1000 genomes]
rs12370707	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12371014	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12422372	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12425735	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1444099	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444102	0.86[ASN][1000 genomes]
rs1568303	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121828	0.86[ASN][1000 genomes]
rs17536893	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17537939	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17627506	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2120527	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55888651	0.86[ASN][1000 genomes]
rs57205785	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58692617	1.00[AFR][1000 genomes]
rs60522760	1.00[AFR][1000 genomes]
rs61919518	1.00[AFR][1000 genomes]
rs61919519	1.00[AFR][1000 genomes]
rs61919520	1.00[AFR][1000 genomes]
rs61919524	1.00[AFR][1000 genomes]
rs61919525	0.82[ASN][1000 genomes]
rs61919531	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs61919532	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs61919550	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61934309	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581224	1.00[AFR][1000 genomes]
rs7136193	1.00[ASW][hapmap];0.81[GIH][hapmap]
rs7138401	1.00[AFR][1000 genomes]
rs7314727	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960109	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7968111	1.00[AFR][1000 genomes]
rs7980955	0.99[EUR][1000 genomes];0.86[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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172898	MBD6	cis	cerebellum	SCAN
rs11172898	PIP4K2C	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59454400-59471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59461400-59465600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:59461400-59468800	Weak transcription	Fetal Stomach	stomach
4	chr12:59461400-59469400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:59461800-59469000	Weak transcription	Fetal Intestine Small	intestine
6	chr12:59462200-59466400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:59463200-59464600	Enhancers	HMEC	breast
8	chr12:59463200-59464800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:59463200-59464800	Enhancers	NHEK	skin
10	chr12:59463200-59465200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:59463200-59465800	Enhancers	Osteobl	bone
12	chr12:59463200-59466000	Enhancers	NH-A	brain
13	chr12:59463400-59464600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:59463400-59464600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:59463400-59465800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:59464000-59464600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:59464000-59464600	Enhancers	Hela-S3	cervix
18	chr12:59464000-59465000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:59464000-59465000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:59464200-59464600	Enhancers	NHLF	lung
21	chr12:59464200-59464800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr12:59464200-59464800	Enhancers	Fetal Lung	lung
23	chr12:59464200-59464800	Flanking Active TSS	HUVEC	blood vessel
24	chr12:59464400-59469000	Weak transcription	Fetal Kidney	kidney

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