Variant report

Variant	rs11169908
Chromosome Location	chr12:39284077-39284078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10506129	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876149	0.84[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876163	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169387	0.84[ASW][hapmap]
rs11169508	0.84[ASW][hapmap]
rs11169769	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169801	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169879	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11609849	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11612004	0.84[ASW][hapmap]
rs11613205	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11615668	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12812262	0.87[CEU][hapmap]
rs12827647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554550	0.84[ASW][hapmap]
rs17464772	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17465893	0.95[CEU][hapmap]
rs17523988	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2056159	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2388060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34204495	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36035670	0.82[EUR][1000 genomes]
rs4332556	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768548	0.82[CEU][hapmap]
rs6580755	0.84[ASW][hapmap]
rs7960621	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967776	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39204000-39284800	Weak transcription	Lung	lung
2	chr12:39269800-39285800	Weak transcription	Osteobl	bone
3	chr12:39271800-39297200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:39277800-39287200	Weak transcription	Aorta	Aorta
5	chr12:39278200-39284400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:39279800-39285800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:39280000-39285600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:39280400-39287200	Weak transcription	Colonic Mucosa	Colon
9	chr12:39280800-39285800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:39281000-39285800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:39281000-39286000	Weak transcription	Gastric	stomach
12	chr12:39282000-39284800	Weak transcription	Right Atrium	heart
13	chr12:39282200-39285800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:39282800-39285200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:39282800-39285200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:39283000-39284600	Enhancers	Stomach Mucosa	stomach
17	chr12:39283200-39284600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:39283200-39285000	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:39283400-39284400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:39283400-39285800	Enhancers	Liver	Liver
21	chr12:39283600-39284600	Enhancers	Colon Smooth Muscle	Colon
22	chr12:39283600-39285800	Weak transcription	Esophagus	oesophagus
23	chr12:39283800-39284400	Weak transcription	Fetal Intestine Small	intestine
24	chr12:39283800-39284600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr12:39283800-39285000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:39283800-39285800	Weak transcription	Left Ventricle	heart
27	chr12:39283800-39285800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:39284000-39284200	Enhancers	Adipose Nuclei	Adipose
29	chr12:39284000-39284400	Flanking Active TSS	A549	lung
30	chr12:39284000-39284400	Enhancers	Hela-S3	cervix
31	chr12:39284000-39284600	Enhancers	HMEC	breast
32	chr12:39284000-39284600	Enhancers	HUVEC	blood vessel
33	chr12:39284000-39284600	Enhancers	NHEK	skin
34	chr12:39284000-39285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links