Variant report

Variant	rs12338262
Chromosome Location	chr9:26800359-26800360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511793	0.82[GIH][hapmap]
rs10812492	0.82[GIH][hapmap]
rs10967594	0.82[GIH][hapmap]
rs12342005	0.80[CEU][hapmap]
rs13288517	0.83[ASN][1000 genomes]
rs16910752	0.84[ASN][1000 genomes]
rs17693846	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17693955	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17755607	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17840677	0.81[ASN][1000 genomes]
rs62542115	0.84[ASN][1000 genomes]
rs62542152	0.81[ASN][1000 genomes]
rs62542155	0.92[ASN][1000 genomes]
rs62544361	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544362	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024415	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7035755	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs7039400	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs7045881	0.85[CEU][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	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12338262	IFT74	Cis_1M	lymphoblastoid	RTeQTL
rs12338262	C9orf82	cis	parietal	SCAN
rs12338262	IFT74	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26797000-26800800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:26797600-26800400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:26800000-26800400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:26800000-26800400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:26800200-26800400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:26800200-26801000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:26800200-26802000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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