Variant report

Variant	rs6582240
Chromosome Location	chr12:41580177-41580178
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10748266	0.82[EUR][1000 genomes]
rs10748267	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10879831	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879858	0.92[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10879867	0.90[JPT][hapmap]
rs1346905	0.83[EUR][1000 genomes]
rs1367601	0.83[EUR][1000 genomes]
rs1367602	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1431100	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs1431102	0.83[EUR][1000 genomes]
rs1431103	0.82[EUR][1000 genomes]
rs1431104	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1431105	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1431106	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1431107	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1431108	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1431109	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1431110	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1431112	0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs1461094	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1527086	0.94[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1864611	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1864612	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1864613	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2116133	0.84[EUR][1000 genomes]
rs2116134	0.86[EUR][1000 genomes]
rs2116135	0.85[EUR][1000 genomes]
rs2163415	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163416	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs2169299	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2405768	0.83[EUR][1000 genomes]
rs2567034	0.80[EUR][1000 genomes]
rs281829	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs281831	0.87[EUR][1000 genomes]
rs281832	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs281837	0.89[EUR][1000 genomes]
rs281839	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs281840	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281841	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs281843	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3847980	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3847981	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3858726	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3911712	0.83[EUR][1000 genomes]
rs4238081	0.82[EUR][1000 genomes]
rs4767999	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768334	0.82[JPT][hapmap]
rs7296581	0.82[EUR][1000 genomes]
rs7303285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305919	0.82[JPT][hapmap]
rs7342366	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7487688	0.83[EUR][1000 genomes]
rs776560	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776561	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776562	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776567	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7954881	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963760	0.89[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7980599	0.83[EUR][1000 genomes]
rs975602	0.94[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[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	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1048124	chr12:41499221-41585315	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a
5	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6582240	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41578600-41580400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:41578800-41581400	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:41579800-41580200	Flanking Active TSS	Colon Smooth Muscle	Colon
4	chr12:41579800-41580400	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:41579800-41582000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:41580000-41580200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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