Variant report

Variant	rs10879019
Chromosome Location	chr12:41092064-41092065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1013929	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10735957	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10748138	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10748142	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10748148	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10784796	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10784797	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10784800	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10879028	0.80[ASN][1000 genomes]
rs10879031	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10879092	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10879095	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11177862	0.83[ASN][1000 genomes]
rs11177863	0.83[ASN][1000 genomes]
rs11177886	0.80[ASN][1000 genomes]
rs11177927	0.80[ASN][1000 genomes]
rs11177954	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11177961	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11178000	0.80[ASN][1000 genomes]
rs11178013	0.80[ASN][1000 genomes]
rs11178015	0.80[ASN][1000 genomes]
rs11178017	0.80[ASN][1000 genomes]
rs11178018	0.80[ASN][1000 genomes]
rs11178027	0.80[ASN][1000 genomes]
rs11178067	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12367287	0.83[ASN][1000 genomes]
rs12367641	0.83[ASN][1000 genomes]
rs12372385	0.80[ASN][1000 genomes]
rs1373425	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1373426	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1584090	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1584094	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1584095	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1584100	0.88[EUR][1000 genomes]
rs1816855	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1992606	0.83[ASN][1000 genomes]
rs2405293	0.83[ASN][1000 genomes]
rs2405294	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2405295	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61915099	0.80[ASN][1000 genomes]
rs61915100	0.80[ASN][1000 genomes]
rs61915101	0.80[ASN][1000 genomes]
rs6581905	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7133642	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7953546	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7960217	0.80[ASN][1000 genomes]
rs7961129	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7962501	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7967298	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971056	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7972371	0.83[ASN][1000 genomes]
rs935224	0.88[EUR][1000 genomes]
rs9783468	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv832378	chr12:40943111-41132305	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2751098	chr12:41082399-41180235	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1044513	chr12:41091822-41175151	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10879019	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx
rs10879019	CNTN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41091400-41092400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:41091400-41093800	Enhancers	HMEC	breast
3	chr12:41091600-41092400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:41091600-41092600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:41091800-41092200	Active TSS	NHEK	skin
6	chr12:41092000-41092800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:41092000-41094800	Enhancers	A549	lung

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