Variant report

Variant	rs11142771
Chromosome Location	chr9:73888408-73888409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11142718	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11142752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11142766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11142784	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035505	chr9:73709852-73934353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv893442	chr9:73778502-74115344	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1052375	chr9:73793681-73893133	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv540152	chr9:73793681-73893133	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv893443	chr9:73859086-74008905	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv916062	chr9:73861614-74246247	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv614605	chr9:73887092-73915883	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11142771	PLEKHA5	trans	lymphoblastoid	seeQTL
rs11142771	TIMP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73886600-73889000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:73887200-73889600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:73887200-73900200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:73887600-73889000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:73887600-73893200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:73888000-73889600	Enhancers	HepG2	liver
7	chr9:73888200-73888600	Enhancers	Stomach Mucosa	stomach
8	chr9:73888400-73888800	Enhancers	Liver	Liver
9	chr9:73888400-73888800	Enhancers	Rectal Mucosa Donor 31	rectum

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