Variant report

Variant	rs11059504
Chromosome Location	chr12:123195036-123195037
allele	G/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	JUND	chr12:123194874-123195301	MCF-7	breast:	n/a	n/a
2	ZNF217	chr12:123194969-123195267	MCF-7	breast:	n/a	n/a
3	GATA3	chr12:123194991-123195209	MCF-7	breast:	n/a	n/a
4	GATA2	chr12:123194868-123195095	SH-SY5Y	brain:	n/a	n/a
5	CEBPB	chr12:123194984-123195338	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr12:123194769-123195325	MCF-7	breast:	n/a	n/a
7	NR2F2	chr12:123194844-123195369	MCF-7	breast:	n/a	n/a
8	GATA3	chr12:123194897-123195387	MCF-7	breast:	n/a	n/a
9	GATA3	chr12:123194628-123195408	MCF-7	breast:	n/a	n/a
10	HDAC2	chr12:123194915-123195367	MCF-7	breast:	n/a	n/a
11	NR2F2	chr12:123194900-123195374	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000256249	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10444445	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773429	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10773433	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10773435	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10773436	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10773445	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10773474	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773515	0.82[ASN][1000 genomes]
rs10773516	0.89[ASN][1000 genomes]
rs10847452	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10847456	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10847570	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10847574	0.89[ASN][1000 genomes]
rs11059356	0.82[AMR][1000 genomes]
rs11059418	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11059507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059583	0.82[ASN][1000 genomes]
rs2088678	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2088682	0.89[ASN][1000 genomes]
rs2649912	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28675952	0.81[AMR][1000 genomes]
rs35173057	0.81[ASN][1000 genomes]
rs531791	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55776099	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61955029	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489204	0.84[AMR][1000 genomes]
rs6489237	0.89[ASN][1000 genomes]
rs7131790	0.82[ASN][1000 genomes]
rs7131791	0.82[ASN][1000 genomes]
rs7133768	0.82[AMR][1000 genomes]
rs7305589	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307192	0.82[ASN][1000 genomes]
rs7309056	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7313367	0.82[ASN][1000 genomes]
rs7958805	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7959072	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7969474	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7970419	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7972971	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][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
rs11059504	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr12:123194400-123195600	Enhancers	Placenta	Placenta
5	chr12:123194400-123196000	Enhancers	NHEK	skin
6	chr12:123194600-123195200	Enhancers	Fetal Intestine Large	intestine
7	chr12:123194800-123195800	Enhancers	HMEC	breast
8	chr12:123195000-123195400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr12:123195000-123195400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:123195000-123195600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:123195000-123195600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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