Variant report

Variant	rs7969238
Chromosome Location	chr12:41231507-41231508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1014167	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1028949	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178978	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12367345	0.85[MEX][hapmap]
rs12578583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12578762	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12579682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580909	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581257	0.90[ASN][1000 genomes]
rs12581462	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12582450	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582480	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12582790	0.90[ASN][1000 genomes]
rs12582806	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12810195	0.90[ASN][1000 genomes]
rs12814216	0.85[ASN][1000 genomes]
rs12824161	0.90[ASN][1000 genomes]
rs34409157	0.90[ASN][1000 genomes]
rs34435345	0.90[ASN][1000 genomes]
rs34480545	0.95[ASN][1000 genomes]
rs34588792	0.90[ASN][1000 genomes]
rs35067046	0.90[ASN][1000 genomes]
rs35640051	0.90[ASN][1000 genomes]
rs35840550	0.90[ASN][1000 genomes]
rs56928815	0.90[ASN][1000 genomes]
rs59969287	0.90[ASN][1000 genomes]
rs7303594	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7307211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310770	0.90[ASN][1000 genomes]
rs7311456	0.90[ASN][1000 genomes]
rs73118754	0.90[ASN][1000 genomes]
rs73118756	0.90[ASN][1000 genomes]
rs7312428	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7314477	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7960431	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7969238	KIF21A	cis	cerebellum	SCAN
rs7969238	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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