Variant report

Variant	rs10407999
Chromosome Location	chr19:42192835-42192836
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42192804..42194422-chr19:42196991..42198512,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1005340	0.94[ASN][1000 genomes]
rs1015758	0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10409040	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417599	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10417970	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418202	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1122493	0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1548725	0.81[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1548726	0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1860328	0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2016070	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2016082	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2052080	0.85[EUR][1000 genomes]
rs2191137	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4239513	0.90[ASN][1000 genomes]
rs4426458	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802126	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803494	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803495	0.88[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803501	0.95[ASN][1000 genomes]
rs6508988	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7248447	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7248956	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7249800	0.95[ASN][1000 genomes]
rs8106661	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110064	0.91[EUR][1000 genomes]
rs9304598	0.98[EUR][1000 genomes];1.00[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	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10407999	IRF3	cis	cerebellum	SCAN
rs10407999	TMEM160	cis	cerebellum	SCAN
rs10407999	NPAS1	cis	cerebellum	SCAN
rs10407999	KCNJ14	cis	parietal	SCAN
rs10407999	GIPR	cis	parietal	SCAN
rs10407999	SCAF1	cis	parietal	SCAN
rs10407999	MYPOP	cis	cerebellum	SCAN
rs10407999	ZNF229	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42191400-42193000	Enhancers	Pancreas	Pancrea
2	chr19:42192000-42193000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:42192400-42200600	Weak transcription	Rectal Mucosa Donor 31	rectum

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