Variant report

Variant	rs11052261
Chromosome Location	chr12:32968923-32968924
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10772002	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772003	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844354	0.90[EUR][1000 genomes]
rs10844355	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844356	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844357	0.80[CEU][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844358	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844360	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844361	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844362	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844365	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844367	0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11052236	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs11052244	0.90[EUR][1000 genomes]
rs11052247	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11052249	0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11052250	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11052251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11052252	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052253	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052255	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11525539	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11533495	0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11534764	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11534765	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11561218	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228193	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12299188	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299276	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580216	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389109	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3789978	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3850972	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850973	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850974	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3907042	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56798911	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133291	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138758	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7138787	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302586	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs73301721	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73301724	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73301773	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7960291	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963034	0.88[ASN][1000 genomes]
rs7974049	0.83[ASN][1000 genomes]
rs7975210	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9988940	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9988941	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9988988	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9989018	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv531961	chr12:32966192-32997952	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11052261	FAM60A	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32941800-33033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:32943800-33026800	Weak transcription	Fetal Kidney	kidney
3	chr12:32944200-32989400	Weak transcription	Hela-S3	cervix
4	chr12:32945800-32972400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:32946000-32973600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:32949200-32975200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:32949200-32987000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:32949200-33007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:32960200-32969200	Weak transcription	Small Intestine	intestine
10	chr12:32961000-32989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:32961400-32969400	Strong transcription	NHEK	skin
12	chr12:32961400-32971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:32961800-32973400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:32961800-32974800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:32962000-32973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:32962200-32969200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:32962200-32974000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:32962400-32970600	Weak transcription	Fetal Stomach	stomach
19	chr12:32962400-32973400	Weak transcription	Gastric	stomach
20	chr12:32962400-32973400	Weak transcription	Right Atrium	heart
21	chr12:32962600-32973400	Weak transcription	Pancreas	Pancrea
22	chr12:32963000-32970600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:32963000-32986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:32964400-32969000	Weak transcription	Fetal Intestine Large	intestine
25	chr12:32964400-32970600	Weak transcription	Left Ventricle	heart
26	chr12:32964400-32973400	Weak transcription	Colonic Mucosa	Colon
27	chr12:32964600-32970200	Weak transcription	HMEC	breast
28	chr12:32965000-32969200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:32965000-32970400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:32965000-32970600	Weak transcription	HepG2	liver
31	chr12:32965000-32972400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:32965000-32977800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:32965000-32996200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:32965400-32972600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:32966600-32977800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr12:32967000-32971000	Strong transcription	Liver	Liver
37	chr12:32967000-32977800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr12:32967000-32979000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:32967400-32972400	Weak transcription	Right Ventricle	heart
40	chr12:32967400-32973600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:32968200-32969200	Weak transcription	Placenta	Placenta
42	chr12:32968400-32973200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:32968400-32977400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:32968800-32969600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:32968800-32970600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:32968800-32971800	Genic enhancers	Fetal Heart	heart

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