Variant report

Variant	rs6138643
Chromosome Location	chr20:25699129-25699130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs35016365	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35364051	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59046052	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6115241	0.90[ASN][1000 genomes]
rs6132851	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6132857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132862	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132864	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138595	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138598	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138599	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138601	0.84[EUR][1000 genomes]
rs6138604	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138611	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138616	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6138622	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138623	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138625	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138631	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138633	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138639	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6138647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138651	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6138653	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs878176	0.83[AMR][1000 genomes];0.84[EUR][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	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS 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
4	nsv525033	chr20:25688001-25730968	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3451414	chr20:25696452-25700550	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	esv17092	chr20:25698651-25707971	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
7	esv3411467	chr20:25698707-25700769	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6138643	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138643	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138643	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6138643	PYGB	cis	Whole Blood	GTEx
rs6138643	GINS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25677800-25701000	Weak transcription	Pancreas	Pancrea
2	chr20:25694000-25700200	Weak transcription	Primary T cells from cord blood	blood
3	chr20:25694200-25705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr20:25697800-25700000	Weak transcription	Gastric	stomach
5	chr20:25698600-25700600	Weak transcription	Ovary	ovary

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