Variant report

Variant	rs2031031
Chromosome Location	chr3:136523397-136523398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10935193	0.87[AMR][1000 genomes]
rs11713817	0.84[AMR][1000 genomes]
rs11713867	0.81[AMR][1000 genomes]
rs28458819	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28877307	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4420814	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4678441	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4678442	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56163507	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56695781	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60574021	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6793936	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6802291	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7621932	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7633629	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9757179	0.83[AMR][1000 genomes];0.82[EUR][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	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
3	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2031031	PCCB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136520200-136525400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:136521600-136524200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:136521800-136523800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:136521800-136523800	Weak transcription	Pancreas	Pancrea
5	chr3:136521800-136527000	Weak transcription	Hela-S3	cervix
6	chr3:136522000-136523800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:136522000-136523800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:136522400-136524800	Enhancers	Placenta	Placenta
9	chr3:136522600-136524000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:136523000-136525400	Enhancers	GM12878-XiMat	blood

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