Variant report

Variant	rs12440463
Chromosome Location	chr15:35409539-35409540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10519978	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13380141	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1380091	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17818230	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1809254	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2068286	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924543	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924550	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495757	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163827	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168206	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8043460	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302308	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350109	chr15:34668106-35534229	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv522411	chr15:34953986-35462981	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1052721	chr15:35381487-35437841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	esv2761867	chr15:35395441-35409539	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12440463	CHRNA7	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:35401200-35415000	Weak transcription	Adipose Nuclei	Adipose
2	chr15:35407000-35412600	Enhancers	Liver	Liver
3	chr15:35407600-35415600	Weak transcription	Pancreas	Pancrea
4	chr15:35407800-35411600	Weak transcription	HepG2	liver
5	chr15:35407800-35412600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:35408200-35410400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr15:35408800-35412600	Enhancers	Fetal Lung	lung
8	chr15:35409000-35409800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr15:35409000-35410000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr15:35409000-35410000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr15:35409000-35410600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr15:35409200-35410000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:35409200-35410400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr15:35409200-35410600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:35409400-35409600	Enhancers	Brain Germinal Matrix	brain
16	chr15:35409400-35409800	Flanking Active TSS	iPS-20b 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