Variant report

Variant	rs2279535
Chromosome Location	chr12:40603316-40603317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10878160	0.85[JPT][hapmap]
rs10878161	0.86[JPT][hapmap]
rs10878162	0.85[JPT][hapmap]
rs10878180	0.86[JPT][hapmap]
rs11612806	0.82[ASN][1000 genomes]
rs1388594	0.85[ASN][1000 genomes]
rs1491932	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1491940	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1491941	0.86[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2131086	0.85[ASN][1000 genomes]
rs2201141	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263419	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2263420	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307016	0.86[JPT][hapmap]
rs2638229	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2638230	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638233	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638272	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708418	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708419	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708420	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708421	0.83[ASN][1000 genomes]
rs2708422	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708424	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708427	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2708435	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2723259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2723261	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4567538	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57944060	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581622	0.80[AMR][1000 genomes]
rs767940	0.85[JPT][hapmap]
rs7969112	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7970326	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973254	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279535	AC079630.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40601400-40604400	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:40601600-40604400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:40602000-40603800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:40602200-40603800	Enhancers	GM12878-XiMat	blood
5	chr12:40602200-40604200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:40602200-40604200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:40602200-40604200	Enhancers	Fetal Kidney	kidney
8	chr12:40602200-40604400	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:40602400-40604000	Enhancers	A549	lung
10	chr12:40602600-40603600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:40602800-40603400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr12:40602800-40603600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:40603000-40603800	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr12:40603000-40604400	Enhancers	Hela-S3	cervix
15	chr12:40603200-40604000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr12:40603200-40604200	Enhancers	Colon Smooth Muscle	Colon
17	chr12:40603200-40605400	Enhancers	Primary monocytes fromperipheralblood	blood

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