Variant report

Variant	rs1878224
Chromosome Location	chr12:39309714-39309715
allele	A/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	REST	chr12:39309566-39309906	PFSK-1	brain:	n/a	n/a
2	TCF12	chr12:39309552-39310035	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:39309580-39310016	PFSK-1	brain:	n/a	n/a
4	GATA3	chr12:39309551-39310086	SH-SY5Y	brain:	n/a	chr12:39309807-39309817 chr12:39309807-39309816 chr12:39309850-39309860
5	EP300	chr12:39309564-39309911	SK-N-SH_RA	brain:	n/a	n/a
6	GATA3	chr12:39309607-39310047	SK-N-SH	brain:	n/a	chr12:39309807-39309817 chr12:39309807-39309816 chr12:39309850-39309860
7	GATA2	chr12:39309574-39310023	SH-SY5Y	brain:	n/a	chr12:39309807-39309817 chr12:39309807-39309816 chr12:39309850-39309860
8	EP300	chr12:39309242-39310199	SK-N-SH	brain:	n/a	chr12:39309249-39309263 chr12:39309347-39309361
9	GATA3	chr12:39309532-39310024	SK-N-SH	brain:	n/a	chr12:39309807-39309817 chr12:39309807-39309816 chr12:39309850-39309860
10	EP300	chr12:39309557-39309922	SK-N-SH_RA	brain:	n/a	n/a
11	TCF12	chr12:39309612-39309953	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39295565..39299427-chr12:39307532..39310185,3	K562	blood:

Variant related genes	Relation type
ENSG00000252801	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10876062	0.85[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10876185	0.80[EUR][1000 genomes]
rs11169878	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11835596	0.89[ASW][hapmap]
rs12422883	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs12424244	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs12424853	0.95[EUR][1000 genomes]
rs12425783	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs12427196	0.80[EUR][1000 genomes]
rs12580722	0.95[EUR][1000 genomes]
rs17126713	0.80[EUR][1000 genomes]
rs1878223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57950648	0.80[EUR][1000 genomes]
rs58235891	0.80[EUR][1000 genomes]
rs58908887	0.83[AFR][1000 genomes]
rs59843534	0.80[EUR][1000 genomes]
rs60409162	0.80[EUR][1000 genomes]
rs60863548	0.80[EUR][1000 genomes]
rs61636003	0.80[EUR][1000 genomes]
rs7138835	0.80[EUR][1000 genomes]
rs7307936	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs73084040	0.80[EUR][1000 genomes]
rs73084066	0.80[EUR][1000 genomes]
rs73084068	0.80[EUR][1000 genomes]
rs7308580	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs73089536	0.80[EUR][1000 genomes]
rs73089574	0.80[EUR][1000 genomes]
rs7954044	0.80[EUR][1000 genomes]
rs7956929	0.95[EUR][1000 genomes]
rs7957071	0.88[AFR][1000 genomes]
rs7968397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908511	0.89[ASW][hapmap];1.00[YRI][hapmap]
rs9943730	1.00[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv2761733	chr12:39309714-39413045	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39308800-39310000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:39309200-39309800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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