Variant report

Variant	rs6080317
Chromosome Location	chr20:16580891-16580892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1105853	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207205	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2328049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813228	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4813229	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4813230	0.92[EUR][1000 genomes]
rs4814513	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4814516	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4814517	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6034549	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6034552	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6034554	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6044161	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6044162	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6044169	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6044170	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6044171	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6044173	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6044174	0.92[EUR][1000 genomes]
rs6075081	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6080303	0.81[CHB][hapmap];0.83[TSI][hapmap]
rs6080312	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6080315	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6080320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6080330	0.95[EUR][1000 genomes]
rs6111200	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6135800	0.81[CHB][hapmap]
rs6135809	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs928624	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs945239	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs945240	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517032	chr20:16560990-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	nsv585650	chr20:16561203-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv1057674	chr20:16564642-16593209	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv2760669	chr20:16564654-16587606	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv1061216	chr20:16564668-16586544	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv1060264	chr20:16565162-16586544	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv3454156	chr20:16566305-16586918	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	esv3454158	chr20:16566325-16586923	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	esv3454157	chr20:16566369-16586867	Bivalent Enhancer Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	esv3454159	chr20:16566398-16586879	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	esv3454160	chr20:16566441-16586777	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv16895	chr20:16566460-16586787	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv3693287	chr20:16567202-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
14	nsv438309	chr20:16567202-16585314	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	nsv458936	chr20:16567202-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv458937	chr20:16567202-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
17	nsv458938	chr20:16567202-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv585651	chr20:16567202-16585314	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv817887	chr20:16567202-16585314	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
20	esv2421920	chr20:16567202-16586634	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
21	nsv470542	chr20:16567202-16588308	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
22	nsv442482	chr20:16568058-16586634	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
23	nsv1057376	chr20:16568062-16586067	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
24	nsv1059010	chr20:16568062-16586544	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
25	nsv1055217	chr20:16568062-16596470	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
26	nsv458939	chr20:16568129-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
27	nsv458941	chr20:16568129-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
28	nsv585652	chr20:16568129-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
29	nsv458942	chr20:16568129-16589003	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
30	nsv585653	chr20:16568129-16589003	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
31	nsv585654	chr20:16568537-16585314	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
32	nsv514935	chr20:16571383-16586590	Enhancers Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
33	nsv1060877	chr20:16575001-16586544	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
34	nsv1061807	chr20:16575463-16586544	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
35	nsv1064197	chr20:16575463-16587230	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
36	nsv1062741	chr20:16575531-16586544	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6080317	C20orf23	cis	multi-tissue	Pritchard
rs6080317	KIF16B	cis	cerebellum	SCAN
rs6080317	C20orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16580400-16582800	Enhancers	Fetal Lung	lung
2	chr20:16580600-16584200	Enhancers	Fetal Brain Male	brain

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