Variant report

Variant	rs1798192
Chromosome Location	chr12:123200768-123200769
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000182782	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1055884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1696352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17884481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798184	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256936	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2257405	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2262194	0.82[ASN][1000 genomes]
rs2454703	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454718	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2454722	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2550	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28710048	0.98[AFR][1000 genomes];0.99[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	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488635	0.82[ASN][1000 genomes]
rs496911	0.89[CHD][hapmap]
rs535010	0.81[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	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs586573	0.84[EUR][1000 genomes]
rs588293	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600501	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs601339	0.95[JPT][hapmap]
rs602293	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs612057	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61955032	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61955034	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631256	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs644626	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs648183	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489222	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs676823	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs680838	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680934	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681317	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71456765	0.87[ASN][1000 genomes]
rs71456771	0.82[ASN][1000 genomes]
rs7966605	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9668547	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9668559	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	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	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
4	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
5	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1798192	GPR109A	cis	lymphoblastoid	seeQTL
rs1798192	NIACR2	cis	Lymphoblastoid	GTEx
rs1798192	GPR109B	cis	lymphoblastoid	seeQTL
rs1798192	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123195400-123202200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:123196200-123200800	Weak transcription	GM12878-XiMat	blood
3	chr12:123198800-123201400	Active TSS	Primary B cells from cord blood	blood
4	chr12:123198800-123201400	Enhancers	NHEK	skin
5	chr12:123199200-123200800	Weak transcription	Spleen	Spleen
6	chr12:123199400-123201000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:123199400-123204600	Weak transcription	HMEC	breast
8	chr12:123199600-123201600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:123199800-123200800	Enhancers	Lung	lung
10	chr12:123200200-123200800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:123200200-123201400	Enhancers	Adipose Nuclei	Adipose
12	chr12:123200200-123204400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:123200200-123204600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:123200200-123205600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:123200400-123200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:123200600-123201000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:123200600-123201000	Flanking Active TSS	Esophagus	oesophagus
18	chr12:123200600-123201200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr12:123200600-123201400	Flanking Active TSS	HepG2	liver
20	chr12:123200600-123201600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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