Variant report

Variant	rs2500420
Chromosome Location	chr20:25381842-25381843
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs2039400	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258671	1.00[AMR][1000 genomes]
rs2258672	1.00[AMR][1000 genomes]
rs2474768	1.00[AMR][1000 genomes]
rs2474770	1.00[AMR][1000 genomes]
rs2474772	1.00[AMR][1000 genomes]
rs2474775	1.00[AMR][1000 genomes]
rs2474776	1.00[AMR][1000 genomes]
rs2482907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482917	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482920	1.00[AMR][1000 genomes]
rs2482922	1.00[AMR][1000 genomes]
rs2482925	1.00[AMR][1000 genomes]
rs2482929	1.00[AMR][1000 genomes]
rs2482939	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482942	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500394	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500396	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500411	1.00[AMR][1000 genomes]
rs2500412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500416	1.00[AFR][1000 genomes]
rs2500419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500429	1.00[AMR][1000 genomes]
rs2500431	1.00[AMR][1000 genomes]
rs2500434	1.00[AMR][1000 genomes]
rs2500437	1.00[AMR][1000 genomes]
rs2500438	1.00[AMR][1000 genomes]
rs2500440	1.00[AMR][1000 genomes]
rs2500444	1.00[AMR][1000 genomes]
rs2500445	1.00[AMR][1000 genomes]
rs2500447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2983490	1.00[AMR][1000 genomes]
rs2990515	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3002699	1.00[AMR][1000 genomes]
rs3002700	1.00[AMR][1000 genomes]
rs3002703	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs364722	1.00[AMR][1000 genomes]
rs366060	1.00[AMR][1000 genomes]
rs368636	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368748	1.00[AMR][1000 genomes]
rs378534	1.00[AMR][1000 genomes]
rs379538	1.00[AMR][1000 genomes]
rs380021	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs384336	1.00[AMR][1000 genomes]
rs400916	1.00[AMR][1000 genomes]
rs423248	1.00[AMR][1000 genomes]
rs426143	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs429120	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432403	1.00[AMR][1000 genomes]
rs439642	1.00[AMR][1000 genomes]
rs442728	1.00[AMR][1000 genomes]
rs448212	1.00[AMR][1000 genomes]
rs448866	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs518336	1.00[AMR][1000 genomes]
rs6037089	1.00[AMR][1000 genomes]
rs6037112	0.87[AFR][1000 genomes]
rs6037113	0.98[AFR][1000 genomes]
rs6037119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050613	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050627	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050628	0.87[AFR][1000 genomes]
rs73904036	1.00[AMR][1000 genomes]
rs73904038	1.00[AMR][1000 genomes]
rs73904039	1.00[AMR][1000 genomes]
rs73904476	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
9	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic 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	16 gene(s)	inside rSNPs	diseases
17	nsv964440	chr20:25351740-25387631	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	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
19	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
20	nsv1059494	chr20:25377602-25441835	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25379800-25382200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:25381600-25382200	Enhancers	HepG2	liver

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