Variant report

Variant	rs2638272
Chromosome Location	chr12:40609883-40609884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10878160	0.85[JPT][hapmap]
rs10878161	0.85[JPT][hapmap]
rs10878162	0.85[JPT][hapmap]
rs10878180	0.85[JPT][hapmap]
rs10878247	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs11612806	0.80[ASN][1000 genomes]
rs1388594	0.83[ASN][1000 genomes]
rs1491932	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1491940	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1491941	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2131086	0.82[ASN][1000 genomes]
rs2201141	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2263419	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2263420	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279535	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307016	0.85[JPT][hapmap]
rs2638229	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638230	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638233	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708418	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708419	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708420	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708421	0.81[ASN][1000 genomes]
rs2708422	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708424	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708427	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2723259	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2723261	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4567538	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57944060	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs767940	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs7969112	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7970326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973254	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2638272	AC079630.2	cis	Esophagus Mucosa	GTEx
rs2638272	ZCRB1	cis	cerebellum	SCAN
rs2638272	ZCRB1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40604200-40611000	Weak transcription	Fetal Kidney	kidney
2	chr12:40605200-40610400	Weak transcription	A549	lung
3	chr12:40608800-40611400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:40609200-40610000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:40609200-40611200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:40609400-40610000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:40609400-40610800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:40609400-40611000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:40609400-40611000	Enhancers	Hela-S3	cervix
10	chr12:40609400-40611000	Enhancers	HMEC	breast
11	chr12:40609600-40610000	Enhancers	Primary B cells from cord blood	blood
12	chr12:40609600-40610000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:40609600-40610400	Enhancers	NHEK	skin
14	chr12:40609600-40610600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:40609600-40611000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:40609800-40610200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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