Variant report

Variant	rs452238
Chromosome Location	chr19:44484993-44484994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10164273	0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10164282	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11666551	0.89[ASN][1000 genomes]
rs11668687	0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11669568	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11669702	0.89[ASN][1000 genomes]
rs11670342	0.89[ASN][1000 genomes]
rs11670772	0.84[EUR][1000 genomes]
rs11671384	0.89[ASN][1000 genomes]
rs11672879	0.86[EUR][1000 genomes]
rs11673170	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12185486	0.89[ASN][1000 genomes]
rs2284242	0.82[ASN][1000 genomes]
rs2284243	0.86[JPT][hapmap]
rs36044624	0.85[EUR][1000 genomes]
rs365745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366111	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs367358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369958	0.89[YRI][hapmap]
rs380242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392160	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs415913	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs425200	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439676	0.93[ASW][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs441794	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442679	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs445265	0.83[EUR][1000 genomes]
rs454218	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458647	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460071	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462417	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55750317	0.84[EUR][1000 genomes]
rs58591332	0.90[EUR][1000 genomes]
rs612663	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61734609	0.89[ASN][1000 genomes]
rs73035922	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73038560	0.82[ASN][1000 genomes]
rs73038602	0.80[ASN][1000 genomes]
rs73050193	0.89[ASN][1000 genomes]
rs73050195	0.89[ASN][1000 genomes]
rs73051806	0.86[ASN][1000 genomes]
rs73051810	0.89[ASN][1000 genomes]
rs73051815	0.89[ASN][1000 genomes]
rs73051825	0.89[ASN][1000 genomes]
rs73051828	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs452238	CCDC114	cis	parietal	SCAN
rs452238	NR1H2	cis	cerebellum	SCAN
rs452238	ZNF234	cis	multi-tissue	Pritchard
rs452238	ZNF616	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44456400-44487800	ZNF genes & repeats	Liver	Liver
2	chr19:44462000-44485200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44474800-44487600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:44480800-44485000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44482200-44487800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:44482600-44487600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:44484400-44487800	Weak transcription	Brain Angular Gyrus	brain
8	chr19:44484800-44485200	ZNF genes & repeats	Aorta	Aorta
9	chr19:44484800-44485200	ZNF genes & repeats	Pancreas	Pancrea

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