Variant report

Variant	rs494794
Chromosome Location	chr6:140507594-140507595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12523815	0.86[EUR][1000 genomes]
rs1390498	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1390499	0.90[CHB][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1416288	0.84[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs188002	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs201281	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap]
rs2050717	0.84[EUR][1000 genomes]
rs532938	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs538875	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs644333	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6570390	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs675432	0.90[CHB][hapmap]
rs702284	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8180615	0.80[ASN][1000 genomes]
rs9321762	0.84[CHB][hapmap];1.00[YRI][hapmap]
rs9376484	0.84[CEU][hapmap]
rs9376507	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9389788	0.87[ASN][1000 genomes]
rs982369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv886693	chr6:140444057-140578494	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv1825718	chr6:140476088-140584384	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs494794	IL22RA2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140497000-140516400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:140505800-140513000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:140506000-140508400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr6:140506000-140511200	Weak transcription	Ovary	ovary
5	chr6:140506200-140508800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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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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