Variant report

Variant	rs4846348
Chromosome Location	chr1:221702709-221702710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10863630	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10863631	0.83[EUR][1000 genomes]
rs11118744	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12074359	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1380252	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1599087	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3911600	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846347	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846718	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61600912	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9725646	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9726206	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9726287	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9727778	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9729477	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9730022	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1009838	chr1:221692621-221773945	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535301	chr1:221692621-221773945	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4846348	TLR5	cis	cerebellum	SCAN
rs4846348	LYPLAL1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221701800-221703400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:221702200-221702800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:221702200-221704000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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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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