Variant report

Variant	rs17113809
Chromosome Location	chr12:74975211-74975212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10785134	0.94[ASN][1000 genomes]
rs10879802	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10879809	0.91[ASN][1000 genomes]
rs11180077	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11180109	0.91[ASN][1000 genomes]
rs11180110	0.93[ASN][1000 genomes]
rs1493836	0.91[ASN][1000 genomes]
rs1493838	0.93[ASN][1000 genomes]
rs2001937	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2613893	0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2641479	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs56778725	0.83[ASN][1000 genomes]
rs6582223	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs68019310	0.84[ASN][1000 genomes]
rs7301245	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7980550	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17113809	TSPAN8	cis	cerebellum	SCAN
rs17113809	CPM	cis	parietal	SCAN
rs17113809	ATXN7L3B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74973400-74980000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:74973800-74978400	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:74974200-74975400	Enhancers	Stomach Mucosa	stomach
4	chr12:74974600-74975400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:74974600-74976000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:74974600-74976000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr12:74974600-74976000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr12:74974800-74975800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr12:74975200-74975800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:74975200-74975800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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