Variant report

Variant	rs12203961
Chromosome Location	chr6:134048964-134048965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1000025	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10485153	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10485154	0.81[ASN][1000 genomes]
rs12210532	0.82[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12216307	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12660662	0.98[ASN][1000 genomes]
rs12660720	0.98[ASN][1000 genomes]
rs12660957	0.84[ASN][1000 genomes]
rs12661599	0.88[ASN][1000 genomes]
rs12717184	0.82[ASN][1000 genomes]
rs13194152	0.90[ASN][1000 genomes]
rs13194345	0.86[ASN][1000 genomes]
rs13196860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200337	0.85[ASN][1000 genomes]
rs13203797	0.85[ASN][1000 genomes]
rs13204047	0.85[ASN][1000 genomes]
rs13219946	0.85[ASN][1000 genomes]
rs1468052	0.92[ASN][1000 genomes]
rs1468053	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1468054	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1476382	0.92[ASN][1000 genomes]
rs17062752	0.82[ASN][1000 genomes]
rs17398008	0.82[ASN][1000 genomes]
rs17398113	0.82[ASN][1000 genomes]
rs17398664	0.86[ASN][1000 genomes]
rs17399159	0.82[ASN][1000 genomes]
rs17476396	0.82[ASN][1000 genomes]
rs1999756	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2069060	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2207405	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2327380	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2327381	0.83[ASN][1000 genomes]
rs34537042	0.92[ASN][1000 genomes]
rs35081309	0.88[ASN][1000 genomes]
rs35317124	0.83[ASN][1000 genomes]
rs35439350	0.85[ASN][1000 genomes]
rs35470523	0.82[ASN][1000 genomes]
rs36055382	0.94[ASN][1000 genomes]
rs36092198	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55952233	0.85[ASN][1000 genomes]
rs59635582	0.89[ASN][1000 genomes]
rs62427563	0.82[ASN][1000 genomes]
rs62429310	0.83[ASN][1000 genomes]
rs6569892	0.80[ASN][1000 genomes]
rs6569894	0.80[ASN][1000 genomes]
rs6569896	0.82[ASN][1000 genomes]
rs6569897	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6569898	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569899	0.85[ASN][1000 genomes]
rs68054668	0.82[ASN][1000 genomes]
rs6904690	0.85[ASN][1000 genomes]
rs6906782	0.88[ASN][1000 genomes]
rs6917316	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6918525	0.88[ASN][1000 genomes]
rs6918884	0.88[ASN][1000 genomes]
rs6919211	0.91[ASN][1000 genomes]
rs6921832	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6925029	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6926195	0.82[ASN][1000 genomes]
rs6939216	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6941465	0.88[ASN][1000 genomes]
rs71576327	0.92[ASN][1000 genomes]
rs736572	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739052	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7739104	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7739428	0.82[ASN][1000 genomes]
rs7739826	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7749675	0.93[ASN][1000 genomes]
rs7767765	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321411	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321412	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9493690	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493692	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493695	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493698	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9493710	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9493712	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9493716	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9493719	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv1032687	chr6:133987372-134059728	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1024201	chr6:133987372-134062162	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830812	chr6:133993897-134165407	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12203961	ALDH8A1	cis	cerebellum	SCAN
rs12203961	TBPL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134043200-134052200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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