Variant report

Variant	rs12282264
Chromosome Location	chr11:66955376-66955377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10791900	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10896161	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896165	0.84[EUR][1000 genomes]
rs11227687	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11227689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs11227690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11227695	0.83[ASN][1000 genomes]
rs11227696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs11227697	0.81[ASN][1000 genomes]
rs11227701	0.88[ASN][1000 genomes]
rs11227703	0.88[ASN][1000 genomes]
rs11227713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs11227715	0.94[ASN][1000 genomes]
rs11227718	0.94[ASN][1000 genomes]
rs11227720	0.94[ASN][1000 genomes]
rs11227722	0.94[ASN][1000 genomes]
rs11227723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs11227732	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11227742	1.00[EUR][1000 genomes]
rs11227744	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11227746	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11227751	1.00[EUR][1000 genomes]
rs11227752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11227755	1.00[JPT][hapmap]
rs11227761	0.84[EUR][1000 genomes]
rs11227770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12271777	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12273711	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12274774	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12293866	0.86[ASN][1000 genomes]
rs17145414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs28604372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3730145	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55936319	0.83[ASN][1000 genomes]
rs58100805	1.00[EUR][1000 genomes]
rs61395951	0.88[ASN][1000 genomes]
rs61758508	0.84[EUR][1000 genomes]
rs61889551	0.84[EUR][1000 genomes]
rs61889552	0.84[EUR][1000 genomes]
rs61891316	0.83[ASN][1000 genomes]
rs61891317	0.83[ASN][1000 genomes]
rs61891340	0.94[ASN][1000 genomes]
rs61891342	0.94[ASN][1000 genomes]
rs61891343	0.91[ASN][1000 genomes]
rs61891344	0.94[ASN][1000 genomes]
rs61891346	0.94[ASN][1000 genomes]
rs6591234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6591235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111473	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7127431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs72926981	0.83[ASN][1000 genomes]
rs7947663	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9630209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12282264	SSH3	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66907800-66975000	Weak transcription	Pancreas	Pancrea
2	chr11:66918800-66968000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:66926000-66966800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:66926200-66963800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:66930800-66985600	Weak transcription	Small Intestine	intestine
6	chr11:66936400-66956000	Weak transcription	Fetal Heart	heart
7	chr11:66936400-67006200	Weak transcription	Stomach Mucosa	stomach
8	chr11:66942600-66982800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:66942800-66961000	Weak transcription	Gastric	stomach
10	chr11:66944000-66961200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:66945000-66956200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:66945000-66956600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr11:66945000-66956800	Strong transcription	Dnd41	blood
14	chr11:66945000-66957000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:66945800-66984800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:66946400-66955400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr11:66947000-66955600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:66947000-66956400	Strong transcription	GM12878-XiMat	blood
19	chr11:66947000-66964000	Strong transcription	Fetal Thymus	thymus
20	chr11:66947200-66957200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:66947200-66957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:66947200-66958400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:66947200-66959400	Strong transcription	Placenta	Placenta
24	chr11:66947400-66955600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr11:66947400-66956400	Strong transcription	Fetal Lung	lung
26	chr11:66947400-66956600	Strong transcription	HMEC	breast
27	chr11:66947400-66957000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr11:66947400-66958000	Strong transcription	Fetal Intestine Large	intestine
29	chr11:66947600-66958200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr11:66947600-66958600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:66947600-66963000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:66948000-66970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:66948200-66962000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:66948200-66975000	Weak transcription	Right Ventricle	heart
35	chr11:66948200-66986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:66948800-66958800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:66949600-66958800	Strong transcription	Fetal Stomach	stomach
38	chr11:66949600-66975000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:66949800-66957000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:66949800-66957400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:66950800-66957000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:66951200-66965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr11:66951200-66975000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:66951200-66975000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr11:66951200-66986600	Weak transcription	Fetal Brain Male	brain
46	chr11:66951400-66957000	Weak transcription	Esophagus	oesophagus
47	chr11:66951600-66968000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:66952400-66963400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:66953000-66975000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:66953400-66957000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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