Variant report

Variant	rs830123
Chromosome Location	chr12:122426217-122426218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122417398..122419986-chr12:122423812..122426379,2	K562	blood:
2	chr12:122398645..122400405-chr12:122425070..122427774,2	K562	blood:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1154510	0.80[MEX][hapmap]
rs1169075	0.91[AMR][1000 genomes]
rs1169077	1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs1169080	0.80[AMR][1000 genomes]
rs1169082	0.89[AMR][1000 genomes]
rs1169085	1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs1169092	0.83[AMR][1000 genomes]
rs1169093	1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs1182927	1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes]
rs1667583	0.90[MEX][hapmap]
rs1720041	1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs1916333	0.83[AMR][1000 genomes]
rs1971955	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493519	0.95[MEX][hapmap]
rs529736	0.86[MEX][hapmap];0.83[TSI][hapmap]
rs59586951	0.83[ASN][1000 genomes]
rs6486794	1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs7314056	0.85[MEX][hapmap]
rs7957207	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs7961103	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs830116	0.82[AMR][1000 genomes]
rs830120	0.86[CEU][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs830122	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs830124	0.95[MEX][hapmap]
rs853758	0.80[AMR][1000 genomes]
rs895958	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs830123	GPR109B	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122409800-122427200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:122409800-122428400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:122409800-122428400	Weak transcription	NHEK	skin
6	chr12:122410000-122428600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:122412800-122430600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:122413200-122428800	Weak transcription	HSMMtube	muscle
9	chr12:122415200-122434800	Weak transcription	Pancreas	Pancrea
10	chr12:122415400-122428400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:122418400-122427000	Weak transcription	Fetal Stomach	stomach
12	chr12:122418800-122437600	Weak transcription	Spleen	Spleen
13	chr12:122419000-122427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:122419800-122429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:122422000-122427200	Weak transcription	GM12878-XiMat	blood
16	chr12:122422200-122429800	Weak transcription	Thymus	Thymus
17	chr12:122422800-122428200	Weak transcription	Fetal Thymus	thymus
18	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
19	chr12:122423000-122428400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:122425000-122428200	Weak transcription	HepG2	liver

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