Variant report

Variant	rs7139273
Chromosome Location	chr12:29434650-29434651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10047562	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1006409	0.83[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1035604	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10771507	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771508	0.96[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10843361	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10843366	0.90[EUR][1000 genomes]
rs10843367	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10843371	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10843373	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10843375	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843377	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs10843382	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs10843384	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10843398	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11050151	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050152	0.86[EUR][1000 genomes]
rs11050153	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050157	0.89[EUR][1000 genomes]
rs11050161	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050162	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050163	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11050167	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11050170	0.85[EUR][1000 genomes]
rs11050181	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs11050187	0.81[EUR][1000 genomes]
rs11050188	0.81[EUR][1000 genomes]
rs11050189	0.80[EUR][1000 genomes]
rs11833737	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228468	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12366505	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs12366527	0.81[EUR][1000 genomes]
rs16934135	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1989478	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1991114	0.82[EUR][1000 genomes]
rs2015599	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2042511	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2194518	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2194519	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2194520	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2216853	0.93[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2216854	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2278094	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs3782506	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs3782509	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs3782511	0.81[CEU][hapmap]
rs4331146	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6487790	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6487796	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6487804	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6487805	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs6487808	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6487815	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs67146951	0.81[EUR][1000 genomes]
rs67150462	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67517901	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7131987	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7294598	0.81[CEU][hapmap]
rs7299861	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7301188	0.89[CEU][hapmap]
rs7302129	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7308125	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7311912	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7312164	0.81[EUR][1000 genomes]
rs7315504	0.86[CHB][hapmap]
rs7316004	0.96[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs737160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954278	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs7954871	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7957339	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7958210	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7970390	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7973786	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7974221	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7976961	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs918873	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs962866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9738721	0.80[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:29420400-29435000	Weak transcription	HUVEC	blood vessel
3	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
4	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:29422200-29434800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:29424600-29435200	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:29424800-29434800	Weak transcription	Dnd41	blood
8	chr12:29425200-29435600	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:29426600-29440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:29426800-29436200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:29426800-29440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:29427000-29435200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
16	chr12:29427800-29438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
18	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:29431800-29434800	Weak transcription	HSMMtube	muscle
21	chr12:29432200-29442800	Weak transcription	Psoas Muscle	Psoas
22	chr12:29432400-29438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:29432600-29434800	Weak transcription	HSMM	muscle
24	chr12:29432600-29435000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:29432600-29436600	Weak transcription	NH-A	brain
26	chr12:29432800-29445800	Weak transcription	Primary B cells from cord blood	blood
27	chr12:29433400-29434800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:29433400-29435400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:29433400-29436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:29433400-29436400	Enhancers	Primary hematopoietic stem cells	blood
31	chr12:29433600-29435400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr12:29434200-29449600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:29434400-29435400	Enhancers	Fetal Kidney	kidney
34	chr12:29434400-29435600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:29434400-29435600	Enhancers	Fetal Stomach	stomach
36	chr12:29434400-29435800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:29434400-29435800	Enhancers	Adipose Nuclei	Adipose
38	chr12:29434400-29439000	Enhancers	Osteobl	bone
39	chr12:29434600-29434800	Enhancers	NHDF-Ad	bronchial
40	chr12:29434600-29436200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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