Variant report

Variant	rs680838
Chromosome Location	chr12:123196572-123196573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1696352	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17884481	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798184	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1798192	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256572	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256936	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257405	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2262194	0.82[ASN][1000 genomes]
rs2454703	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454718	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2550	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28710048	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3104613	0.80[ASN][1000 genomes]
rs3104614	0.80[ASN][1000 genomes]
rs34699072	0.82[ASN][1000 genomes]
rs488391	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488635	0.82[ASN][1000 genomes]
rs535010	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537527	0.82[ASN][1000 genomes]
rs55718746	0.85[ASN][1000 genomes]
rs574413	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs586573	0.84[EUR][1000 genomes]
rs588293	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600501	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602293	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs612057	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61955032	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61955034	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631256	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs644626	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs648183	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489222	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71456765	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71456771	0.82[ASN][1000 genomes]
rs7966605	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9668547	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9668559	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv973132	chr12:123184783-123201537	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	esv8582	chr12:123186451-123200127	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	esv3504363	chr12:123186465-123200093	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	esv3504374	chr12:123186465-123200093	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	esv3493297	chr12:123187437-123200966	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
7	esv3493308	chr12:123187437-123200966	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3348872	chr12:123192296-123213461	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs680838	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123174000-123199800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:123187800-123198600	Weak transcription	Adipose Nuclei	Adipose
3	chr12:123192600-123199800	Weak transcription	HepG2	liver
4	chr12:123195400-123196600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:123195400-123198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:123195400-123202200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:123195600-123198800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:123195600-123200000	Weak transcription	Placenta	Placenta
9	chr12:123195800-123198800	Weak transcription	HMEC	breast
10	chr12:123196000-123197200	Weak transcription	NHEK	skin
11	chr12:123196200-123198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:123196200-123200800	Weak transcription	GM12878-XiMat	blood
13	chr12:123196400-123198800	Enhancers	Monocytes-CD14+_RO01746	blood

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