Variant report

Variant	rs3131020
Chromosome Location	chr6:29475902-29475903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1557819	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1557820	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1592410	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1592411	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2107188	0.98[EUR][1000 genomes]
rs2107190	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2158281	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2189372	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2859876	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094565	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094566	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094570	0.90[EUR][1000 genomes]
rs3094571	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130860	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3131021	0.82[AFR][1000 genomes]
rs3131022	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757256	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	esv3424039	chr6:29439297-29504564	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv883528	chr6:29447724-29494897	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv883529	chr6:29464365-29494897	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3131020	SLC17A3	cis	parietal	SCAN
rs3131020	ZSCAN23	cis	parietal	SCAN
rs3131020	HMGN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29468600-29496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29475200-29477800	Enhancers	GM12878-XiMat	blood
3	chr6:29475800-29476000	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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