Variant report

Variant	rs11904880
Chromosome Location	chr20:52419174-52419175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000225563	TF binding region
ENSG00000008405	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000257548	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10211779	0.82[AFR][1000 genomes]
rs10211840	0.83[AFR][1000 genomes]
rs10211844	0.83[AFR][1000 genomes]
rs10211847	0.83[AFR][1000 genomes]
rs16998448	0.83[AFR][1000 genomes]
rs2870289	0.83[AFR][1000 genomes]
rs6097589	0.83[AFR][1000 genomes]
rs6097590	0.83[AFR][1000 genomes]
rs6097593	0.83[AFR][1000 genomes]
rs6097594	0.83[AFR][1000 genomes]
rs6097596	0.83[AFR][1000 genomes]
rs6097597	0.83[AFR][1000 genomes]
rs6097598	0.83[AFR][1000 genomes]
rs6097602	1.00[AMR][1000 genomes]
rs7273809	0.83[AFR][1000 genomes]
rs73272042	0.83[AFR][1000 genomes]
rs73272044	0.80[AFR][1000 genomes]
rs73272049	0.83[AFR][1000 genomes]
rs8126424	0.83[AFR][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
7	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52411800-52421400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52412200-52421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:52414000-52421800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:52416000-52425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr20:52416600-52419400	Weak transcription	HMEC	breast
6	chr20:52417400-52420600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:52418000-52423400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr20:52418200-52421600	Enhancers	A549	lung
9	chr20:52418400-52422600	Enhancers	HepG2	liver
10	chr20:52418400-52422800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr20:52418600-52422400	Weak transcription	Fetal Intestine Small	intestine
12	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
13	chr20:52418800-52419200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:52418800-52421800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:52419000-52419400	Weak transcription	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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