Variant report

Variant	rs612057
Chromosome Location	chr12:123184550-123184551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1696352	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17884481	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1798184	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1798192	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2256572	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256936	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2257405	0.83[ASN][1000 genomes]
rs2454703	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2454718	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2550	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28710048	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488391	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs535010	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs574413	0.80[AMR][1000 genomes]
rs586573	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs588293	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs600501	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602293	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61955034	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs631256	0.82[AMR][1000 genomes]
rs644626	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs648183	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6489222	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680838	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs680934	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs681317	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71456765	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7966605	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9668547	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9668559	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13329	chr12:123178106-123210671	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	esv3379602	chr12:123179885-123191721	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	esv3336946	chr12:123180291-123193845	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	esv8843	chr12:123181591-123195219	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	esv1834041	chr12:123184235-123187305	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs612057	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123166600-123187800	Weak transcription	A549	lung
2	chr12:123174000-123199800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:123181800-123185400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:123182600-123185200	Weak transcription	Adipose Nuclei	Adipose
5	chr12:123182600-123185200	Weak transcription	HMEC	breast
6	chr12:123182600-123185400	Weak transcription	NHEK	skin
7	chr12:123182800-123185200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:123183000-123185000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:123183000-123185200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:123183000-123185400	Weak transcription	Placenta	Placenta
11	chr12:123183800-123184800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr12:123184000-123188800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:123184200-123185800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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