Variant report

Variant	rs169639
Chromosome Location	chr20:52595491-52595492
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs12479580	0.81[JPT][hapmap]
rs2024066	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs208362	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs208367	0.88[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs208368	0.81[YRI][hapmap]
rs208379	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs208389	0.80[CHD][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap]
rs2276507	0.81[JPT][hapmap]
rs2276510	0.83[ASW][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs431061	0.80[CEU][hapmap]
rs6013861	0.80[AMR][1000 genomes];0.86[EUR][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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52580800-52600000	Weak transcription	Stomach Mucosa	stomach
3	chr20:52581200-52610600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52591200-52597000	Strong transcription	HSMMtube	muscle
5	chr20:52592000-52599600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:52592800-52599600	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:52593000-52600800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:52593200-52601000	Weak transcription	Brain Substantia Nigra	brain
9	chr20:52595200-52596400	Strong transcription	Rectal Mucosa Donor 31	rectum

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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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