Variant report

Variant	rs574413
Chromosome Location	chr12:123194673-123194674
allele	C/T
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	GATA3	chr12:123194628-123195408	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000256249	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1696352	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17884481	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1798184	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1798192	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2256572	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2256936	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2454703	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2454718	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2550	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28710048	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs488391	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs588293	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs600501	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs602293	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs612057	0.80[AMR][1000 genomes]
rs61955034	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs631256	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs648183	0.84[EUR][1000 genomes]
rs6489222	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs680838	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs680934	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs681317	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71456765	0.81[AMR][1000 genomes]
rs9668547	0.85[AMR][1000 genomes]
rs9668559	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	esv3486411	chr12:123186029-123195050	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	esv3486412	chr12:123186029-123195050	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	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
7	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
8	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
9	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
10	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
11	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
rs574413	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 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	chr12:123190400-123195000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:123192600-123199800	Weak transcription	HepG2	liver
5	chr12:123194200-123194800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:123194400-123195600	Enhancers	Placenta	Placenta
7	chr12:123194400-123196000	Enhancers	NHEK	skin
8	chr12:123194600-123195200	Enhancers	Fetal Intestine Large	intestine

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