Variant report

Variant	rs2016082
Chromosome Location	chr19:42152918-42152919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1005340	0.89[ASN][1000 genomes]
rs1015758	0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10407999	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]
rs10409040	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10417599	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10417970	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418202	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1122493	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1548725	0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs1548726	0.86[ASN][1000 genomes]
rs1860328	0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2016070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052080	0.85[EUR][1000 genomes]
rs2191137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239513	0.86[ASN][1000 genomes]
rs4426458	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802126	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803495	0.87[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803501	0.90[ASN][1000 genomes]
rs6508988	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7248447	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248956	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7249800	0.90[ASN][1000 genomes]
rs8106661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110064	0.91[EUR][1000 genomes]
rs9304598	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058847	chr19:42057334-42172442	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1063241	chr19:42057334-42175160	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv519408	chr19:42066279-42171906	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2016082	IRF3	cis	cerebellum	SCAN
rs2016082	GIPR	cis	parietal	SCAN
rs2016082	TMEM160	cis	cerebellum	SCAN
rs2016082	ZNF229	cis	parietal	SCAN
rs2016082	MYPOP	cis	cerebellum	SCAN
rs2016082	SCAF1	cis	parietal	SCAN
rs2016082	KCNJ14	cis	parietal	SCAN
rs2016082	NPAS1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42151800-42153600	Enhancers	Colonic Mucosa	Colon
2	chr19:42151800-42155200	Enhancers	Stomach Mucosa	stomach
3	chr19:42152200-42153600	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr19:42152200-42155200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr19:42152600-42154000	Enhancers	Rectal Mucosa Donor 29	rectum

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