Variant report

Variant	rs6138609
Chromosome Location	chr20:25570985-25570986
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr20:25570851-25571092	K562	blood:	n/a	n/a

Variant related genes	Relation type
NINL	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1047171	0.82[EUR][1000 genomes]
rs11087520	0.84[EUR][1000 genomes]
rs11087521	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11699203	0.84[EUR][1000 genomes]
rs12428	0.82[EUR][1000 genomes]
rs13038834	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1541061	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1985737	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2104734	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2151144	0.83[EUR][1000 genomes]
rs2179459	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2387881	0.80[EUR][1000 genomes]
rs2387885	0.84[EUR][1000 genomes]
rs2387887	0.82[EUR][1000 genomes]
rs2387891	0.88[EUR][1000 genomes]
rs2424712	0.82[EUR][1000 genomes]
rs2424713	0.82[EUR][1000 genomes]
rs2424714	0.82[EUR][1000 genomes]
rs2424715	0.81[EUR][1000 genomes]
rs2424716	0.84[EUR][1000 genomes]
rs2482911	0.81[EUR][1000 genomes]
rs2482913	0.81[EUR][1000 genomes]
rs2482918	0.83[EUR][1000 genomes]
rs2482943	0.80[EUR][1000 genomes]
rs2500417	0.80[EUR][1000 genomes]
rs2500418	0.80[EUR][1000 genomes]
rs2500424	0.81[EUR][1000 genomes]
rs2500436	0.81[EUR][1000 genomes]
rs2500448	0.81[EUR][1000 genomes]
rs2856	0.82[EUR][1000 genomes]
rs372678	0.88[EUR][1000 genomes]
rs397119	0.84[EUR][1000 genomes]
rs398036	0.84[EUR][1000 genomes]
rs401166	0.84[EUR][1000 genomes]
rs404394	0.84[EUR][1000 genomes]
rs408853	0.83[EUR][1000 genomes]
rs416745	0.84[EUR][1000 genomes]
rs417110	0.87[EUR][1000 genomes]
rs417130	0.88[EUR][1000 genomes]
rs422424	0.84[EUR][1000 genomes]
rs422844	0.84[EUR][1000 genomes]
rs424487	0.87[EUR][1000 genomes]
rs4280527	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs431579	0.87[EUR][1000 genomes]
rs433352	0.87[EUR][1000 genomes]
rs437635	0.87[EUR][1000 genomes]
rs442834	0.87[EUR][1000 genomes]
rs446649	0.87[EUR][1000 genomes]
rs447722	0.84[EUR][1000 genomes]
rs448396	0.84[EUR][1000 genomes]
rs449370	0.86[EUR][1000 genomes]
rs449703	0.87[EUR][1000 genomes]
rs453329	0.84[EUR][1000 genomes]
rs454723	0.84[EUR][1000 genomes]
rs4815424	0.81[EUR][1000 genomes]
rs6037120	0.84[EUR][1000 genomes]
rs6037121	0.82[EUR][1000 genomes]
rs6037125	0.88[EUR][1000 genomes]
rs6037126	0.87[EUR][1000 genomes]
rs6050609	0.81[EUR][1000 genomes]
rs6050611	0.84[EUR][1000 genomes]
rs6050617	0.82[EUR][1000 genomes]
rs6050626	0.81[EUR][1000 genomes]
rs6050629	0.81[EUR][1000 genomes]
rs6050630	0.82[EUR][1000 genomes]
rs6050631	0.84[EUR][1000 genomes]
rs6050632	0.82[EUR][1000 genomes]
rs6083853	0.80[EUR][1000 genomes]
rs6083856	0.81[EUR][1000 genomes]
rs6083862	0.81[EUR][1000 genomes]
rs6107044	0.82[EUR][1000 genomes]
rs6107045	0.84[EUR][1000 genomes]
rs6107046	0.84[EUR][1000 genomes]
rs6107047	0.84[EUR][1000 genomes]
rs6107052	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6115182	0.81[EUR][1000 genomes]
rs6115183	0.80[EUR][1000 genomes]
rs6115185	0.81[EUR][1000 genomes]
rs6115191	0.84[EUR][1000 genomes]
rs6115200	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6115204	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6115214	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6115215	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6115218	0.86[AFR][1000 genomes]
rs6115229	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132833	0.84[EUR][1000 genomes]
rs6132835	0.82[EUR][1000 genomes]
rs6132848	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138571	0.84[EUR][1000 genomes]
rs6138572	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138575	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138588	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6138600	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6515651	0.84[EUR][1000 genomes]
rs7270835	0.84[EUR][1000 genomes]
rs761025	0.84[EUR][1000 genomes]
rs8113919	0.81[EUR][1000 genomes]
rs84816	0.84[EUR][1000 genomes]
rs928121	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6138609	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138609	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138609	ABHD12	cis	Esophagus Muscularis	GTEx
rs6138609	PYGB	cis	Whole Blood	GTEx
rs6138609	PYGB	cis	multi-tissue	Pritchard
rs6138609	ABHD12	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25566800-25572600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr20:25566800-25573200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25567000-25574200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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