Variant report

Variant	rs10425196
Chromosome Location	chr19:53726975-53726976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10401578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10404048	0.82[CHB][hapmap]
rs10424778	0.82[ASN][1000 genomes]
rs10775558	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853858	0.89[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853859	0.80[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11084227	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084228	0.85[ASN][1000 genomes]
rs1129002	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs1136205	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666631	0.93[ASN][1000 genomes]
rs11672812	0.81[ASN][1000 genomes]
rs11672910	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11673594	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12972588	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12982260	0.85[ASN][1000 genomes]
rs12984188	0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs12984473	0.94[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs12985503	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17272966	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs28411117	0.86[ASN][1000 genomes]
rs28734122	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2914371	0.91[CHB][hapmap]
rs2914372	0.88[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs2914376	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs2914377	0.85[ASN][1000 genomes]
rs2914378	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs2914381	0.82[CHB][hapmap]
rs2914383	0.88[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs2965221	0.81[CHB][hapmap]
rs2965222	0.85[ASN][1000 genomes]
rs2965223	0.81[CHB][hapmap]
rs2965224	0.82[CHB][hapmap]
rs2965230	0.80[CHB][hapmap]
rs2965231	0.82[CHB][hapmap]
rs2965236	0.85[ASN][1000 genomes]
rs2965237	0.85[ASN][1000 genomes]
rs2965238	0.85[ASN][1000 genomes]
rs2965240	0.85[ASN][1000 genomes]
rs2965242	0.88[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs3097248	0.85[ASN][1000 genomes]
rs3111319	0.85[ASN][1000 genomes]
rs36114232	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801965	0.94[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs4801968	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4801970	0.80[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803069	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803071	0.87[ASN][1000 genomes]
rs4803080	0.85[ASN][1000 genomes]
rs55779655	0.87[ASN][1000 genomes]
rs59782712	0.86[ASN][1000 genomes]
rs62117782	0.86[ASN][1000 genomes]
rs62117787	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62117791	0.84[ASN][1000 genomes]
rs71363315	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247982	0.87[CHB][hapmap]
rs8113436	0.85[ASN][1000 genomes]
rs9788	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10425196	ZNF587	cis	cerebellum	SCAN
rs10425196	LIG1	trans	cerebellum	SCAN
rs10425196	ZNF547	cis	cerebellum	SCAN
rs10425196	OSCAR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53725000-53727000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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