Variant report

Variant	rs17702546
Chromosome Location	chr17:66615999-66616000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1116782	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17702693	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28665123	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35002536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815357	0.87[CHB][hapmap]
rs56378596	0.80[ASN][1000 genomes]
rs62087515	0.83[ASN][1000 genomes]
rs8077301	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs986099	0.83[ASN][1000 genomes]
rs9896434	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9908210	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9915927	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17702546	ABCA6	cis	parietal	SCAN
rs17702546	AMZ2	cis	parietal	SCAN
rs17702546	AMZ2P1	cis	parietal	SCAN
rs17702546	ABCA9	cis	parietal	SCAN
rs17702546	ICAM2	cis	parietal	SCAN
rs17702546	FTSJ3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66609000-66621000	Weak transcription	Esophagus	oesophagus
2	chr17:66609400-66617000	Weak transcription	Osteobl	bone
3	chr17:66610000-66624200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:66612000-66616600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr17:66615000-66616200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr17:66615200-66617400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:66615600-66616400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:66615600-66617400	Enhancers	Primary neutrophils fromperipheralblood	blood

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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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