Variant report

Variant	rs1822598
Chromosome Location	chr12:41231443-41231444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10784898	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784901	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879294	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879339	0.81[ASN][1000 genomes]
rs10879340	0.81[ASN][1000 genomes]
rs11178530	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11178848	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11178979	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1126373	0.92[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12317351	0.85[ASN][1000 genomes]
rs12371725	0.82[ASN][1000 genomes]
rs1579194	0.82[ASN][1000 genomes]
rs1584097	0.80[EUR][1000 genomes]
rs1822599	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184321	0.82[ASN][1000 genomes]
rs1928561	0.82[ASN][1000 genomes]
rs2034159	0.83[AFR][1000 genomes]
rs2583991	0.82[ASN][1000 genomes]
rs2583992	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2772459	0.80[AFR][1000 genomes]
rs2772461	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2772478	0.87[ASN][1000 genomes]
rs2772479	0.80[ASN][1000 genomes]
rs312270	0.82[ASN][1000 genomes]
rs312271	0.82[ASN][1000 genomes]
rs312274	0.80[ASN][1000 genomes]
rs312276	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs312283	0.82[ASN][1000 genomes]
rs4360771	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4768312	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66578805	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7134512	0.81[AFR][1000 genomes]
rs7300719	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300865	0.81[AFR][1000 genomes]
rs73118764	0.82[ASN][1000 genomes]
rs7487913	0.87[EUR][1000 genomes]
rs7967262	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913831	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325193	0.83[AFR][1000 genomes]
rs984129	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1822598	CNTN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41226800-41266400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:41229400-41235400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:41231000-41232000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:41231400-41232000	ZNF genes & repeats	Pancreas	Pancrea

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