Variant report

Variant	rs12990877
Chromosome Location	chr2:55710494-55710495
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11125576	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11680106	0.86[ASN][1000 genomes]
rs11694644	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12612931	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12620109	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12988721	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12989168	0.99[ASN][1000 genomes]
rs13011640	0.99[ASN][1000 genomes]
rs13012151	0.90[ASN][1000 genomes]
rs13012554	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13028756	0.83[ASN][1000 genomes]
rs13030415	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008040	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2061031	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2061032	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs34076674	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72917934	0.98[ASN][1000 genomes]
rs7600456	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs957267	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12990877	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55706400-55714600	Weak transcription	K562	blood
2	chr2:55708400-55711200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:55709400-55711000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:55709400-55711200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:55709600-55711200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55709800-55710800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:55709800-55710800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:55710000-55710800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:55710000-55711000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:55710000-55716800	Weak transcription	HUES6 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