Variant report

Variant	rs13290672
Chromosome Location	chr9:13959282-13959283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10961339	0.86[JPT][hapmap]
rs13283743	0.86[JPT][hapmap]
rs13294545	0.83[ASN][1000 genomes]
rs13299961	0.89[ASN][1000 genomes]
rs17192702	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17278798	0.86[JPT][hapmap]
rs36092776	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55776100	0.89[ASN][1000 genomes]
rs66840986	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7023574	0.85[JPT][hapmap]
rs71511072	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72715813	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022001	chr9:13717736-13983738	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv613635	chr9:13893246-13961462	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1015319	chr9:13931836-13970419	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv613636	chr9:13936438-13975480	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv3423193	chr9:13956977-13959525	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
8	esv3439330	chr9:13957152-13959450	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13290672	SNAPC3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13933600-13961600	Weak transcription	Psoas Muscle	Psoas
2	chr9:13940400-13962000	Weak transcription	Left Ventricle	heart
3	chr9:13956600-13962200	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:13957400-13960000	Weak transcription	Adipose Nuclei	Adipose
5	chr9:13957400-13960000	Weak transcription	Fetal Heart	heart
6	chr9:13957800-13961400	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:13958600-13960400	Enhancers	Fetal Lung	lung
8	chr9:13958800-13959600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:13958800-13963600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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