Variant report

Variant	rs9567825
Chromosome Location	chr13:47865088-47865089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11841943	0.87[ASN][1000 genomes]
rs2406324	0.98[ASN][1000 genomes]
rs2406325	0.99[ASN][1000 genomes]
rs2406326	1.00[ASN][1000 genomes]
rs2406327	1.00[ASN][1000 genomes]
rs4531630	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4567609	0.88[ASN][1000 genomes]
rs509160	0.88[EUR][1000 genomes]
rs6561367	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7320852	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999656	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs8001945	0.94[ASN][1000 genomes]
rs9526304	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9526306	0.99[ASN][1000 genomes]
rs9526307	0.92[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[ASN][1000 genomes]
rs9534581	0.89[ASN][1000 genomes]
rs9534584	0.80[ASN][1000 genomes]
rs9534593	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763019	chr13:47348229-48123447	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3394678	chr13:47678184-48039379	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832599	chr13:47703075-47873855	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9567825	KCTD4	cis	cerebellum	SCAN
rs9567825	DLEU2	cis	cerebellum	SCAN
rs9567825	C13orf31	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:47862800-47874200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:47863200-47865400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:47864200-47865800	Enhancers	Hela-S3	cervix
4	chr13:47864400-47865200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	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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