Variant report

Variant	rs10843561
Chromosome Location	chr12:30073931-30073932
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1007811	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10771594	0.84[AMR][1000 genomes]
rs10771595	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10771597	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10771598	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771599	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843530	0.83[AMR][1000 genomes]
rs10843532	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10843533	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10843535	0.81[EUR][1000 genomes]
rs10843540	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843541	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843542	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843543	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843544	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050510	0.83[AMR][1000 genomes]
rs11050517	0.80[EUR][1000 genomes]
rs11050522	0.81[EUR][1000 genomes]
rs11050531	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050532	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050533	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050548	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12302114	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1545889	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1564772	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564773	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2129141	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4606557	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4623987	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487854	0.81[AMR][1000 genomes]
rs6487855	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6487856	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6487857	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6487858	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6487859	0.81[EUR][1000 genomes]
rs6487860	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132925	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7134717	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7134917	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7136379	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7294362	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7308012	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308200	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962173	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971964	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972136	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972251	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979975	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7980162	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7980933	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv469191	chr12:29939628-30098770	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv557958	chr12:29939628-30098770	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv526146	chr12:29989292-30112823	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2758302	chr12:30023167-30175232	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2759889	chr12:30023167-30175232	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10843561	C12orf72	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30073600-30074800	Enhancers	Fetal Heart	heart
2	chr12:30073600-30075000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:30073800-30074400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:30073800-30074800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:30073800-30074800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:30073800-30074800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:30073800-30074800	Enhancers	Hela-S3	cervix
8	chr12:30073800-30074800	Enhancers	HMEC	breast
9	chr12:30073800-30075000	Enhancers	HUVEC	blood vessel

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