Variant report

Variant	rs11520080
Chromosome Location	chr12:59251262-59251263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10877180	0.86[EUR][1000 genomes]
rs11172717	0.82[AMR][1000 genomes]
rs11172730	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172731	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172737	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172739	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172742	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172759	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172771	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172773	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172774	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172775	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172777	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172779	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172780	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172783	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172784	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172786	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172787	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172790	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11172791	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1148531	0.84[EUR][1000 genomes]
rs11514001	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11514217	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11514219	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11514220	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11514221	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11520079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11520081	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11520082	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11520084	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367092	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12367116	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12368328	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369527	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12370599	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12371811	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12372281	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17121505	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17121548	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17121569	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17121576	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17121582	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279718	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2293659	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55920960	0.89[ASN][1000 genomes]
rs74099519	0.85[AFR][1000 genomes]
rs74099636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74099638	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv899126	chr12:59199972-59255857	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1038273	chr12:59232371-59259628	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3440532	chr12:59244734-59266539	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59235600-59252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:59243000-59257600	Weak transcription	NH-A	brain
3	chr12:59243200-59263600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:59245200-59257400	Weak transcription	NHDF-Ad	bronchial
5	chr12:59245200-59260000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:59248800-59251600	Enhancers	Fetal Intestine Small	intestine
7	chr12:59249400-59253600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:59250200-59252800	Enhancers	Stomach Mucosa	stomach
9	chr12:59250200-59255400	Enhancers	Fetal Intestine Large	intestine
10	chr12:59250400-59257800	Weak transcription	Gastric	stomach
11	chr12:59250800-59251400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:59250800-59251400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:59250800-59251600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:59250800-59252000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:59251000-59266400	Weak transcription	Esophagus	oesophagus
16	chr12:59251200-59251600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
17	chr12:59251200-59257800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:59251200-59261800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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