Variant report

Variant	rs164840
Chromosome Location	chr5:106962349-106962350
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs154190	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs164685	0.99[ASN][1000 genomes]
rs164687	0.89[ASN][1000 genomes]
rs164838	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs164841	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180791	0.81[CHB][hapmap]
rs26727	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs26731	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.88[ASN][1000 genomes]
rs26736	0.86[CEU][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap]
rs352614	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352615	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs35552	0.86[CEU][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap]
rs469425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs164840	PPY	trans	cerebellum	SCAN
rs164840	EFNA5	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106942400-106981600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:106944600-106969200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:106954200-106967600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:106954400-106968800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:106955400-106969000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:106956000-106968200	Weak transcription	A549	lung
7	chr5:106956600-106962600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:106960200-106962400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:106960200-106964200	Weak transcription	Fetal Heart	heart
10	chr5:106961400-106966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:106962000-106963800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:106962200-106962600	Enhancers	ES-UCSF4 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