Variant report

Variant	rs3940638
Chromosome Location	chr12:41056749-41056750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10161138	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10161509	0.81[ASN][1000 genomes]
rs10748138	0.81[ASN][1000 genomes]
rs10748142	0.83[ASN][1000 genomes]
rs10879028	0.84[ASN][1000 genomes]
rs10879079	0.81[ASN][1000 genomes]
rs11177589	0.84[EUR][1000 genomes]
rs11177809	0.92[ASN][1000 genomes]
rs11177862	0.87[ASN][1000 genomes]
rs11177863	0.87[ASN][1000 genomes]
rs11177886	0.84[ASN][1000 genomes]
rs11177927	0.84[ASN][1000 genomes]
rs11178000	0.84[ASN][1000 genomes]
rs11178013	0.84[ASN][1000 genomes]
rs11178015	0.84[ASN][1000 genomes]
rs11178017	0.84[ASN][1000 genomes]
rs11178018	0.84[ASN][1000 genomes]
rs11178027	0.84[ASN][1000 genomes]
rs11178070	0.81[ASN][1000 genomes]
rs12296967	0.81[ASN][1000 genomes]
rs12367287	0.87[ASN][1000 genomes]
rs12367641	0.87[ASN][1000 genomes]
rs12372385	0.84[ASN][1000 genomes]
rs1816855	0.83[ASN][1000 genomes]
rs1918951	0.81[ASN][1000 genomes]
rs1918953	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1992606	0.87[ASN][1000 genomes]
rs2405290	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2405293	0.87[ASN][1000 genomes]
rs2405295	0.83[ASN][1000 genomes]
rs61915074	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61915099	0.84[ASN][1000 genomes]
rs61915100	0.84[ASN][1000 genomes]
rs61915101	0.84[ASN][1000 genomes]
rs61915102	0.81[ASN][1000 genomes]
rs6581905	0.85[ASN][1000 genomes]
rs7311914	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73267740	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7960217	0.84[ASN][1000 genomes]
rs7967298	0.85[ASN][1000 genomes]
rs7971056	0.83[ASN][1000 genomes]
rs7972371	0.87[ASN][1000 genomes]
rs7974939	0.92[ASN][1000 genomes]
rs935224	0.86[ASN][1000 genomes]
rs9669757	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3940638	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41056400-41056800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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