Variant report

Variant	rs9890441
Chromosome Location	chr17:66600045-66600046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12452734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs12940313	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2907385	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs9675199	1.00[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9890441	ABCA9	cis	parietal	SCAN
rs9890441	ABCA6	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66597600-66600200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr17:66598400-66601200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr17:66598600-66600400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr17:66598800-66600400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr17:66598800-66602200	Weak transcription	Liver	Liver
6	chr17:66599400-66604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:66599600-66600200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr17:66599600-66600200	Enhancers	Placenta	Placenta
9	chr17:66599600-66600400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr17:66599600-66601600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:66599800-66601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:66600000-66600200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr17:66600000-66600200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr17:66600000-66600400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr17:66600000-66601200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:66600000-66601200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:66600000-66602000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr17:66600000-66604000	Weak transcription	H1 Cell Line	embryonic stem cell

Quick Search:

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

what's new

Quick links