Variant report

Variant	rs10743652
Chromosome Location	chr12:29408007-29408008
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1006410	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs10450679	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1052583	0.81[CEU][hapmap]
rs10743651	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10743656	0.86[YRI][hapmap]
rs10771512	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10843365	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843372	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843402	0.90[JPT][hapmap]
rs11050168	0.82[CHB][hapmap];0.87[YRI][hapmap]
rs11050200	0.82[CEU][hapmap]
rs1120528	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12301475	0.80[AFR][1000 genomes]
rs17715086	0.82[CHB][hapmap]
rs1991113	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2059362	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2194517	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288128	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs2288129	0.82[CHB][hapmap];0.87[YRI][hapmap]
rs2882294	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3782505	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs3782507	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3782508	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3948497	0.80[CHB][hapmap]
rs4370971	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4412790	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487789	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6487791	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6487792	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487795	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487796	0.81[CEU][hapmap]
rs6487797	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487799	0.89[EUR][1000 genomes]
rs6487800	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487802	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487803	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7134187	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7137141	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7295056	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7295212	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298031	0.87[YRI][hapmap]
rs7299283	0.82[CHB][hapmap];0.87[YRI][hapmap]
rs7299648	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299772	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7300032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7301575	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7302399	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303960	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73063614	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7308534	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7311081	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316026	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs766445	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953619	0.86[YRI][hapmap]
rs7954375	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954990	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7964831	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs7968167	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7968883	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7971296	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972032	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs7974254	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976227	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976667	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9669514	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9738165	0.87[AMR][1000 genomes];0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10743652	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29396800-29413200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:29400800-29411400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:29406400-29410000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:29406600-29408400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:29406800-29409200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:29407200-29408200	Weak transcription	Left Ventricle	heart
7	chr12:29407400-29408400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr12:29407400-29408800	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:29407400-29409800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:29407800-29408800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:29408000-29408200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:29408000-29408200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:29408000-29408200	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:29408000-29408200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:29408000-29408200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr12:29408000-29408400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:29408000-29408400	Enhancers	Adipose Nuclei	Adipose
18	chr12:29408000-29408400	Enhancers	Right Ventricle	heart
19	chr12:29408000-29409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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