Variant report

Variant	rs12982159
Chromosome Location	chr19:44964300-44964301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2117383	1.00[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap]
rs2140111	0.92[ASN][1000 genomes]
rs2254344	1.00[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap]
rs2571044	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2571054	0.88[ASN][1000 genomes]
rs2571060	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571111	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2686768	0.86[MEX][hapmap]
rs2686770	1.00[CHB][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2686771	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2686775	1.00[CHB][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs2686777	1.00[CHB][hapmap]
rs2686778	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686780	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs542150	0.94[ASN][1000 genomes]
rs565819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs567620	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs630469	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9710256	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv524201	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv525472	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv960853	chr19:44958445-44982821	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv978867	chr19:44963452-44982821	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12982159	SYNGR4	cis	cerebellum	SCAN
rs12982159	IRF3	cis	parietal	SCAN
rs12982159	KLK2	cis	parietal	SCAN
rs12982159	KLK13	cis	cerebellum	SCAN
rs12982159	TSKS	cis	parietal	SCAN
rs12982159	KLC3	cis	cerebellum	SCAN
rs12982159	SNORD35A	cis	parietal	SCAN
rs12982159	RTN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44961000-44964400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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