Variant report

Variant	rs13080353
Chromosome Location	chr3:140875814-140875815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1010717	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108693	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1154783	0.84[EUR][1000 genomes]
rs12494491	0.86[EUR][1000 genomes]
rs12631017	1.00[LWK][hapmap]
rs13062081	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13092595	0.89[EUR][1000 genomes]
rs13092946	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1511382	0.84[EUR][1000 genomes]
rs1564257	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683397	0.84[EUR][1000 genomes]
rs4683566	0.87[EUR][1000 genomes]
rs4683570	0.88[EUR][1000 genomes]
rs4683572	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7632817	0.92[EUR][1000 genomes]
rs872329	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9860331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995783	0.84[EUR][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	nsv877550	chr3:140867094-140933231	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13080353	MRPS22	cis	parietal	SCAN
rs13080353	ACPL2	cis	parietal	SCAN
rs13080353	XRN1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140861000-140880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:140866800-140876600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:140870200-140876000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:140872400-140876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:140872600-140877200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:140873000-140876800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:140875200-140878200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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