Variant report

Variant	rs28386802
Chromosome Location	chr2:209234694-209234695
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	CEBPB	chr2:209234443-209234834	IMR90	lung:	n/a	n/a
2	FOS	chr2:209234425-209234873	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr2:209234499-209234713	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr2:209234466-209235022	IMR90	lung:	n/a	n/a
5	STAT3	chr2:209234464-209234771	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr2:209234359-209234960	SK-N-SH	brain:	n/a	n/a
7	FOXA2	chr2:209234366-209236242	HepG2	liver:	n/a	n/a
8	PBX3	chr2:209234462-209234907	SK-N-SH	brain:	n/a	n/a
9	MYC	chr2:209234567-209234780	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr2:209234475-209234853	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:209234325-209234980	SK-N-SH	brain:	n/a	n/a
12	FOS	chr2:209234499-209234862	MCF10A-Er-Src	breast:	n/a	n/a
13	FOSL2	chr2:209234400-209234966	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr2:209234271-209234974	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr2:209234567-209234785	MCF10A-Er-Src	breast:	n/a	n/a
16	GATA3	chr2:209234269-209234963	SK-N-SH	brain:	n/a	n/a
17	FOSL2	chr2:209234502-209234789	A549	lung:	n/a	n/a
18	TCF12	chr2:209234318-209234897	SK-N-SH	brain:	n/a	n/a
19	FOS	chr2:209234417-209234787	MCF10A-Er-Src	breast:	n/a	n/a
20	MYC	chr2:209234500-209234700	MCF10A-Er-Src	breast:	n/a	n/a
21	JUND	chr2:209234418-209234970	SK-N-SH	brain:	n/a	n/a
22	JUND	chr2:209234277-209234996	SK-N-SH	brain:	n/a	n/a
23	FOS	chr2:209234461-209234824	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000265454	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10181047	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10189412	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10189419	0.96[EUR][1000 genomes]
rs11692738	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12617089	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619470	0.95[ASN][1000 genomes]
rs12694110	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003574	0.99[EUR][1000 genomes]
rs13394289	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35444703	0.99[EUR][1000 genomes]
rs4673402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675762	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675763	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675764	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6711995	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6728530	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733145	0.95[ASN][1000 genomes]
rs6745659	0.99[EUR][1000 genomes]
rs6757231	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67608809	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7582376	0.84[EUR][1000 genomes]
rs7586020	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7590641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv437315	chr2:209204714-209249613	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv997721	chr2:209228673-209247209	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1006323	chr2:209228673-209247384	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3418149	chr2:209233519-209247345	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3459072	chr2:209233567-209247320	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3459073	chr2:209233591-209247266	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3459074	chr2:209233591-209247266	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv9904	chr2:209233686-209247332	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28386802	PTH2R	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209220200-209235200	Weak transcription	K562	blood
2	chr2:209233000-209240200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:209233200-209234800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:209233400-209236600	Enhancers	HepG2	liver
5	chr2:209233800-209236600	Enhancers	NHDF-Ad	bronchial
6	chr2:209234000-209236000	Weak transcription	Pancreas	Pancrea
7	chr2:209234000-209236200	Enhancers	Osteobl	bone
8	chr2:209234000-209236600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:209234200-209234800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:209234200-209235000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:209234200-209235000	Enhancers	Placenta	Placenta
12	chr2:209234200-209236200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:209234400-209234800	Flanking Active TSS	Liver	Liver
14	chr2:209234600-209234800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:209234600-209234800	Enhancers	NH-A	brain

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