Variant report

Variant	rs7963760
Chromosome Location	chr12:41631105-41631106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10506182	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10748267	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10785165	0.81[CEU][hapmap]
rs10785177	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs10785186	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs10879831	0.88[ASN][1000 genomes]
rs10879858	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879867	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10879889	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11180421	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11180448	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs12829840	0.83[ASN][1000 genomes]
rs1367600	0.85[CEU][hapmap]
rs1405548	0.88[CEU][hapmap]
rs1431104	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431110	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431112	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.96[ASN][1000 genomes]
rs1431113	0.81[CEU][hapmap]
rs1431114	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs1431115	0.83[CEU][hapmap]
rs1461094	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1527086	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1852461	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs1864611	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864613	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1870704	0.85[CEU][hapmap]
rs1966609	0.81[CEU][hapmap]
rs2043134	0.81[CEU][hapmap]
rs2060053	0.85[CEU][hapmap]
rs2060055	0.85[CEU][hapmap]
rs2163416	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2195706	0.84[EUR][1000 genomes]
rs281832	0.84[AMR][1000 genomes]
rs281839	0.82[AMR][1000 genomes]
rs281840	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs281843	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2897228	0.84[EUR][1000 genomes]
rs3847980	0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs3847981	0.81[EUR][1000 genomes]
rs3858726	0.81[EUR][1000 genomes]
rs4238081	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767999	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768334	0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4768335	0.81[CEU][hapmap]
rs6582240	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]
rs6582280	0.84[EUR][1000 genomes]
rs6582281	0.84[EUR][1000 genomes]
rs6582282	0.84[EUR][1000 genomes]
rs6582283	0.84[EUR][1000 genomes]
rs7137842	0.84[EUR][1000 genomes]
rs7303285	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];0.89[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7305919	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs7342366	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs776560	0.80[AMR][1000 genomes]
rs776562	0.82[AMR][1000 genomes]
rs7954881	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961657	0.84[EUR][1000 genomes]
rs975602	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	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	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
5	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
6	nsv469364	chr12:41631105-41710912	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv558699	chr12:41631105-41710912	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7963760	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41623200-41635600	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41623600-41637000	Weak transcription	Ovary	ovary
3	chr12:41630600-41635600	Weak transcription	Stomach Smooth Muscle	stomach

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