Variant report

Variant	rs9905728
Chromosome Location	chr17:17564523-17564524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4925062	0.83[EUR][1000 genomes]
rs7225141	0.82[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs8067800	0.82[ASN][1000 genomes]
rs9899364	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907751	chr17:17530554-17581184	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9905728	TOM1L2	cis	parietal	SCAN
rs9905728	SMCR3	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17560800-17566200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:17564000-17564600	Enhancers	Pancreas	Pancrea
3	chr17:17564200-17564600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr17:17564200-17564600	Enhancers	Fetal Lung	lung
5	chr17:17564200-17564600	Enhancers	Ovary	ovary
6	chr17:17564200-17566400	Enhancers	HepG2	liver
7	chr17:17564400-17564600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:17564400-17564600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:17564400-17564600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr17:17564400-17564600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:17564400-17564600	Enhancers	Esophagus	oesophagus
12	chr17:17564400-17564600	Enhancers	Gastric	stomach
13	chr17:17564400-17564600	Enhancers	Spleen	Spleen
14	chr17:17564400-17564800	Enhancers	Fetal Heart	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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