Variant report

Variant	rs2302040
Chromosome Location	chr20:52591831-52591832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000178096	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000233786	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs208382	1.00[CEU][hapmap];0.93[GIH][hapmap]
rs208390	0.90[JPT][hapmap]
rs2276495	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs2276505	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2299724	0.82[ASN][1000 genomes]
rs2299732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs391906	1.00[CEU][hapmap]
rs6123333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6123334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73622290	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73622291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr20:52578600-52592400	Weak transcription	Brain Hippocampus Middle	brain
4	chr20:52578800-52592400	Weak transcription	Brain Substantia Nigra	brain
5	chr20:52580800-52600000	Weak transcription	Stomach Mucosa	stomach
6	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr20:52590800-52592200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr20:52591200-52597000	Strong transcription	HSMMtube	muscle
9	chr20:52591400-52592000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr20:52591800-52592600	Enhancers	Brain Anterior Caudate	brain
11	chr20:52591800-52593000	Enhancers	Brain Inferior Temporal Lobe	brain

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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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