Variant report

Variant	rs6022993
Chromosome Location	chr20:52779247-52779248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000257453	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000232638	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1477739	1.00[EUR][1000 genomes]
rs16999399	1.00[EUR][1000 genomes]
rs2219732	1.00[EUR][1000 genomes]
rs2616329	1.00[EUR][1000 genomes]
rs2616331	1.00[EUR][1000 genomes]
rs2616334	1.00[EUR][1000 genomes]
rs2616337	1.00[EUR][1000 genomes]
rs2797969	1.00[EUR][1000 genomes]
rs55972874	1.00[EUR][1000 genomes]
rs6022882	1.00[MEX][hapmap]
rs6022994	1.00[EUR][1000 genomes]
rs61338465	1.00[AMR][1000 genomes]
rs8114866	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1058882	chr20:52765979-52794372	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52768800-52790200	Transcr. at gene 5' and 3'	A549	lung
2	chr20:52769200-52789400	Weak transcription	Esophagus	oesophagus
3	chr20:52769600-52785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52771200-52786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:52777800-52784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:52778800-52784600	Weak transcription	HepG2	liver
7	chr20:52779000-52779400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:52779000-52779400	Active TSS	Brain Anterior Caudate	brain
9	chr20:52779000-52779400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
10	chr20:52779000-52779800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:52779200-52779400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:52779200-52779400	Enhancers	Brain Cingulate Gyrus	brain

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Input of quick search could be:

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

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