Variant report

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10778357	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861292	0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10861297	0.80[EUR][1000 genomes]
rs12230601	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248978	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2252839	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2468095	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2468398	0.81[AMR][1000 genomes]
rs3890816	1.00[CEU][hapmap]
rs4257060	0.89[CEU][hapmap]
rs4630370	0.89[CEU][hapmap]
rs4964116	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964305	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57987047	0.83[EUR][1000 genomes]
rs7133934	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7965314	0.87[AMR][1000 genomes]
rs7973707	0.89[AMR][1000 genomes];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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4409923	C12orf42	cis	cerebellum	SCAN
rs4409923	C12orf23	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105338200-105351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105342600-105350600	Weak transcription	Adipose Nuclei	Adipose
3	chr12:105346800-105351400	Weak transcription	Small Intestine	intestine
4	chr12:105347200-105350600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:105347200-105350600	Enhancers	Liver	Liver
6	chr12:105347400-105350600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:105347400-105350600	Weak transcription	HepG2	liver
8	chr12:105347400-105350800	Weak transcription	NHEK	skin
9	chr12:105347400-105351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:105347600-105350000	Weak transcription	GM12878-XiMat	blood
11	chr12:105347800-105350800	Weak transcription	Hela-S3	cervix
12	chr12:105347800-105351000	Weak transcription	HUVEC	blood vessel
13	chr12:105348200-105349600	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:105348200-105349600	Enhancers	A549	lung
15	chr12:105348400-105350600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:105348400-105350600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:105348800-105349400	Enhancers	Placenta	Placenta
18	chr12:105349000-105349400	Enhancers	Aorta	Aorta
19	chr12:105349000-105349400	Enhancers	Pancreas	Pancrea
20	chr12:105349200-105349400	Enhancers	Fetal Brain Male	brain
21	chr12:105349200-105350200	Enhancers	Stomach Mucosa	stomach

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