Variant report

Variant	rs12125986
Chromosome Location	chr1:63333431-63333432
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10493328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493329	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789127	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789128	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889367	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889377	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889378	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889379	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889380	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889381	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208015	0.91[ASN][1000 genomes]
rs11208016	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11208017	0.83[AMR][1000 genomes]
rs11208029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208041	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208042	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208044	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208048	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208054	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11208055	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061691	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066108	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066524	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067646	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078873	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12080049	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083738	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12084633	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085400	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12085401	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087034	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096696	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12097658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116959	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117272	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12121207	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125325	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129322	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12132170	0.91[ASN][1000 genomes]
rs12133142	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12135672	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136636	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123817	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123830	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123896	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123899	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927485	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927486	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803244	0.83[EUR][1000 genomes]
rs3737891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4409690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55835075	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936326	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55954926	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56280875	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56305462	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56329995	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56935211	0.83[ASN][1000 genomes]
rs57653096	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58583743	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59317258	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60528349	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765883	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587988	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658682	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416683	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513999	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546879	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943696	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830015	chr1:63261143-63455296	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12125986	ATG4C	cis	cerebellum	SCAN
rs12125986	DOCK7	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63298400-63345800	Weak transcription	Left Ventricle	heart
2	chr1:63310000-63340600	Weak transcription	Brain Substantia Nigra	brain
3	chr1:63312000-63335200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:63312200-63335000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:63324200-63334000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:63326600-63333800	Weak transcription	Primary B cells from cord blood	blood
7	chr1:63333400-63333600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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