Variant report

Variant	rs2024063
Chromosome Location	chr20:52612854-52612855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1016279	0.92[JPT][hapmap]
rs10485440	0.92[JPT][hapmap]
rs12480106	0.92[JPT][hapmap]
rs2024064	0.92[JPT][hapmap]
rs2108456	0.91[JPT][hapmap]
rs2276496	0.92[JPT][hapmap]
rs3815270	0.92[JPT][hapmap]
rs431061	0.91[JPT][hapmap]
rs714514	0.91[JPT][hapmap]
rs8120953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124068	0.92[JPT][hapmap]
rs872923	1.00[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs872924	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2024063	C20orf106	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52601800-52630800	Weak transcription	Stomach Mucosa	stomach
3	chr20:52604400-52618200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52612200-52614400	Enhancers	Brain Hippocampus Middle	brain
5	chr20:52612200-52614600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr20:52612200-52614800	Enhancers	Brain Substantia Nigra	brain
7	chr20:52612400-52613400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:52612400-52613600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:52612400-52614400	Enhancers	Brain Anterior Caudate	brain
10	chr20:52612400-52614600	Enhancers	Brain Cingulate Gyrus	brain
11	chr20:52612600-52613000	Weak transcription	Brain Angular Gyrus	brain
12	chr20:52612600-52618600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr20:52612800-52613200	Flanking Active TSS	HSMMtube	muscle

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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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