Variant report

Variant	rs1156816
Chromosome Location	chr19:40133438-40133439
allele	C/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	STAT3	chr19:40133348-40133525	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000268243	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10406803	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418390	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423087	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775536	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083526	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083527	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1156815	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673427	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12608711	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609214	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985763	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985764	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079510	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108390	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214978	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2354228	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2354229	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2883386	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3842958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4286215	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4352162	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4361050	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4461191	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4474814	0.84[EUR][1000 genomes]
rs4577215	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4638715	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802052	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803275	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803281	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803282	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508880	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508881	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508882	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508893	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6508897	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs717348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247678	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251220	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101132	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8104520	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104655	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8105238	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109704	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110098	0.82[ASN][1000 genomes]
rs8111940	0.89[CHB][hapmap]
rs886843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1062653	chr19:40123868-40163241	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv2482	chr19:40125797-40170766	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3413868	chr19:40130700-40184720	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv817835	chr19:40132825-40162019	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1156816	CYP2S1	cis	parietal	SCAN
rs1156816	GSK3A	cis	parietal	SCAN
rs1156816	ZNF230	cis	parietal	SCAN
rs1156816	ZNF404	cis	cerebellum	SCAN
rs1156816	PGLYRP1	cis	cerebellum	SCAN
rs1156816	PLA2G4C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40131800-40133600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr19:40133200-40151200	Weak transcription	Placenta	Placenta

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