Variant report

Variant	rs2454703
Chromosome Location	chr12:123203731-123203732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr12:123203568-123203966	GM12878	blood:	n/a	n/a
2	BATF	chr12:123203623-123203925	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
HCAR3	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1696352	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17884481	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1798184	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1798192	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256572	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256936	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2257405	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2262194	0.80[ASN][1000 genomes]
rs2454718	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2550	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28710048	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34699072	0.80[ASN][1000 genomes]
rs488391	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488635	0.80[ASN][1000 genomes]
rs535010	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs537527	0.80[ASN][1000 genomes]
rs55718746	0.86[ASN][1000 genomes]
rs574413	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs588293	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600501	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602293	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs612057	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61955034	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs631256	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs644626	0.87[ASN][1000 genomes]
rs648183	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489222	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs680838	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs680934	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681317	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71456765	0.84[ASN][1000 genomes]
rs71456771	0.80[ASN][1000 genomes]
rs7966605	0.83[ASN][1000 genomes]
rs9668547	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9668559	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs2454703	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123199400-123204600	Weak transcription	HMEC	breast
2	chr12:123200200-123204400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:123200200-123204600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:123200200-123205600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:123200800-123207800	Weak transcription	Lung	lung
6	chr12:123201000-123207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123201200-123206600	Weak transcription	Esophagus	oesophagus
8	chr12:123201200-123214600	Weak transcription	Spleen	Spleen
9	chr12:123201400-123204200	Weak transcription	Adipose Nuclei	Adipose
10	chr12:123201400-123204600	Weak transcription	NHEK	skin
11	chr12:123201400-123206400	Weak transcription	Fetal Thymus	thymus
12	chr12:123201400-123209400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:123201400-123210000	Weak transcription	Primary B cells from cord blood	blood
14	chr12:123201600-123204600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:123201600-123204800	Weak transcription	Hela-S3	cervix
16	chr12:123202000-123204800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:123202200-123204200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:123202200-123204800	Weak transcription	HepG2	liver
19	chr12:123202400-123204200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:123203200-123204800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:123203400-123204800	Enhancers	GM12878-XiMat	blood
22	chr12:123203400-123206600	Weak transcription	Right Atrium	heart

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