Variant report

Variant	rs9535776
Chromosome Location	chr13:52433564-52433565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1054515	0.84[MEX][hapmap]
rs1886322	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7325195	0.82[EUR][1000 genomes]
rs7326982	0.97[ASN][1000 genomes]
rs7350659	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs932914	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9526797	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526802	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535779	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535780	0.80[EUR][1000 genomes]
rs9591437	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596596	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596598	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535776	NCRNA00282	cis	cerebellum	SCAN
rs9535776	THSD1	cis	cerebellum	SCAN
rs9535776	LOC440138	cis	multi-tissue	Pritchard
rs9535776	CKAP2	cis	cerebellum	SCAN
rs9535776	CKAP2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52430600-52436000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr13:52432600-52433800	Enhancers	HepG2	liver
3	chr13:52432800-52433800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:52433400-52433800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:52433400-52433800	Enhancers	A549	lung
6	chr13:52433400-52434200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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

what's new

Quick links