Variant report

Variant	rs2405295
Chromosome Location	chr12:41097386-41097387
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013929	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10161138	0.89[ASN][1000 genomes]
rs10735957	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10748138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748142	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748148	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784796	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784797	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784800	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879019	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879028	0.99[ASN][1000 genomes]
rs10879031	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879079	0.96[ASN][1000 genomes]
rs10879092	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10879095	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879131	0.86[ASN][1000 genomes]
rs11177809	0.90[ASN][1000 genomes]
rs11177862	0.96[ASN][1000 genomes]
rs11177863	0.96[ASN][1000 genomes]
rs11177886	0.99[ASN][1000 genomes]
rs11177927	0.99[ASN][1000 genomes]
rs11177954	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11177961	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11178000	0.99[ASN][1000 genomes]
rs11178013	0.99[ASN][1000 genomes]
rs11178015	0.99[ASN][1000 genomes]
rs11178017	0.99[ASN][1000 genomes]
rs11178018	0.99[ASN][1000 genomes]
rs11178027	0.99[ASN][1000 genomes]
rs11178050	0.93[ASN][1000 genomes]
rs11178067	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11178070	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11178118	0.93[ASN][1000 genomes]
rs11178122	0.93[ASN][1000 genomes]
rs12367287	0.96[ASN][1000 genomes]
rs12367641	0.96[ASN][1000 genomes]
rs12367708	0.86[ASN][1000 genomes]
rs12372385	0.99[ASN][1000 genomes]
rs1373425	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1373426	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1584090	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1584094	0.84[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1584095	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1584100	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1596538	0.84[ASN][1000 genomes]
rs1816855	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899829	0.81[ASN][1000 genomes]
rs1992606	0.96[ASN][1000 genomes]
rs2405293	0.96[ASN][1000 genomes]
rs2405294	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3940638	0.83[ASN][1000 genomes]
rs61915074	0.86[ASN][1000 genomes]
rs61915099	0.99[ASN][1000 genomes]
rs61915100	0.99[ASN][1000 genomes]
rs61915101	0.99[ASN][1000 genomes]
rs61915102	0.96[ASN][1000 genomes]
rs6581905	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7133642	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139243	0.93[ASN][1000 genomes]
rs7311914	0.86[ASN][1000 genomes]
rs7312935	0.93[ASN][1000 genomes]
rs7953546	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7960217	0.99[ASN][1000 genomes]
rs7961129	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962501	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967298	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971056	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972371	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7974939	0.90[ASN][1000 genomes]
rs935224	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9669757	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9783468	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv558696	chr12:41092666-41172010	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2405295	CNTN1	cis	normal skin	skin_eQTL
rs2405295	CNTN1	cis	lesional skin	skin_eQTL
rs2405295	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx
rs2405295	CNTN1	cis	uninvolved skin	skin_eQTL
rs2405295	CNTN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41092800-41121400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:41093800-41121000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:41096200-41097400	Weak transcription	A549	lung
4	chr12:41097200-41097400	Enhancers	Pancreatic Islets	Pancreatic Islet

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