Variant report

Variant	rs3843476
Chromosome Location	chr5:5031963-5031964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr5:5031757-5032005	U2OS	brain:	n/a	n/a
2	ZNF274	chr5:5031634-5032208	GM08714	blood:	n/a	n/a
3	CHD2	chr5:5031782-5032140	K562	blood:	n/a	n/a
4	ZNF274	chr5:5031789-5032262	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:5021569..5024371-chr5:5031180..5034159,2	K562	blood:

Variant related genes	Relation type
LINC01020	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10042432	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11134088	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11949438	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11955765	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11955794	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003929	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003930	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs249450	0.87[ASN][1000 genomes]
rs249473	0.83[ASN][1000 genomes]
rs35972265	0.86[ASN][1000 genomes]
rs458084	0.83[ASN][1000 genomes]
rs459126	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4620002	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs465871	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs466185	0.86[ASN][1000 genomes]
rs4701651	0.83[ASN][1000 genomes]
rs6555326	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6874575	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6896834	0.86[ASN][1000 genomes]
rs7704552	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021653	chr5:4932992-5201887	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2757980	chr5:4980876-5184615	Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2759318	chr5:4980876-5184615	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv880436	chr5:4982643-5038540	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830194	chr5:5002459-5187667	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv968868	chr5:5024532-5032779	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links