Variant report

Variant	rs28710048
Chromosome Location	chr12:123201539-123201540
allele	C/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	STAT3	chr12:123201005-123201706	MCF10A-Er-Src	breast:	n/a	chr12:123201099-123201120 chr12:123201246-123201253
2	POU2F2	chr12:123201226-123201725	GM12878	blood:	n/a	n/a
3	ZNF384	chr12:123201192-123201602	GM12878	blood:	n/a	n/a
4	FOS	chr12:123201311-123201553	MCF10A-Er-Src	breast:	n/a	n/a
5	NFIC	chr12:123201269-123201756	GM12878	blood:	n/a	n/a
6	FOXA1	chr12:123201319-123201712	HepG2	liver:	n/a	chr12:123201498-123201510
7	RUNX3	chr12:123201185-123201635	GM12878	blood:	n/a	n/a
8	MYC	chr12:123201202-123201616	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr12:123201339-123201555	Hela-S3	cervix:	n/a	chr12:123201448-123201462 chr12:123201446-123201460 chr12:123201449-123201463 chr12:123201447-123201461
10	CEBPB	chr12:123201306-123201554	HepG2	liver:	n/a	n/a
11	CEBPB	chr12:123201228-123201618	Hela-S3	cervix:	n/a	n/a
12	HEY1	chr12:123201086-123201570	HepG2	liver:	n/a	n/a
13	POU2F2	chr12:123201375-123201573	GM12878	blood:	n/a	n/a
14	STAT3	chr12:123201310-123201560	Hela-S3	cervix:	n/a	n/a
15	FOXA1	chr12:123201308-123201576	HepG2	liver:	n/a	chr12:123201498-123201510
16	FOXA1	chr12:123201284-123201752	HepG2	liver:	n/a	chr12:123201498-123201510
17	EBF1	chr12:123201314-123201665	GM12878	blood:	n/a	chr12:123201513-123201524
18	STAT3	chr12:123201311-123201618	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr12:123200968-123201679	MCF10A-Er-Src	breast:	n/a	chr12:123201099-123201120 chr12:123201246-123201253
20	FOS	chr12:123201245-123201623	MCF10A-Er-Src	breast:	n/a	n/a
21	EBF1	chr12:123201339-123201684	GM12878	blood:	n/a	chr12:123201513-123201524
22	STAT3	chr12:123201177-123201692	MCF10A-Er-Src	breast:	n/a	chr12:123201246-123201253
23	CEBPB	chr12:123201328-123201540	A549	lung:	n/a	n/a
24	HDAC2	chr12:123201334-123201559	HepG2	liver:	n/a	chr12:123201448-123201462 chr12:123201445-123201459 chr12:123201450-123201464 chr12:123201447-123201461 chr12:123201449-123201463 chr12:123201444-123201458 chr12:123201446-123201460
25	POU2F2	chr12:123201293-123201714	GM12878	blood:	n/a	n/a
26	EBF1	chr12:123201300-123201698	GM12878	blood:	n/a	chr12:123201513-123201524
27	FOXA2	chr12:123201302-123201579	HepG2	liver:	n/a	chr12:123201498-123201510
28	FOS	chr12:123201325-123201547	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr12:123201183-123201677	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123201536..123203616-chr12:123208338..123210644,2	MCF-7	breast:
2	chr12:123186486..123188573-chr12:123199930..123201817,2	MCF-7	breast:

Variant related genes	Relation type
HCAR3	TF binding region
ENSG00000182782	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1696352	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17884481	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1798184	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1798192	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256936	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2257405	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2262194	0.82[ASN][1000 genomes]
rs2454703	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2454718	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2550	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34699072	0.82[ASN][1000 genomes]
rs488391	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs488635	0.82[ASN][1000 genomes]
rs535010	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537527	0.82[ASN][1000 genomes]
rs55718746	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs574413	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs586573	0.82[EUR][1000 genomes]
rs588293	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600501	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs602293	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs612057	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61955032	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61955034	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631256	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs644626	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs648183	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489222	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs680838	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680934	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681317	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71456765	0.87[ASN][1000 genomes]
rs71456771	0.82[ASN][1000 genomes]
rs7966605	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9668547	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9668559	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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
rs28710048	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123195400-123202200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:123199400-123204600	Weak transcription	HMEC	breast
3	chr12:123199600-123201600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:123200200-123204400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:123200200-123204600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:123200200-123205600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:123200600-123201600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr12:123200800-123207800	Weak transcription	Lung	lung
9	chr12:123201000-123201600	Flanking Active TSS	Hela-S3	cervix
10	chr12:123201000-123207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:123201200-123202400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr12:123201200-123206600	Weak transcription	Esophagus	oesophagus
13	chr12:123201200-123214600	Weak transcription	Spleen	Spleen
14	chr12:123201400-123202000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:123201400-123202200	Enhancers	HepG2	liver
16	chr12:123201400-123203400	Weak transcription	GM12878-XiMat	blood
17	chr12:123201400-123204200	Weak transcription	Adipose Nuclei	Adipose
18	chr12:123201400-123204600	Weak transcription	NHEK	skin
19	chr12:123201400-123206400	Weak transcription	Fetal Thymus	thymus
20	chr12:123201400-123209400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:123201400-123210000	Weak transcription	Primary B cells from cord blood	blood

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