Variant report

Variant	rs554843
Chromosome Location	chr5:113654597-113654598
allele	G/T
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]
rs11241274	0.88[ASN][1000 genomes]
rs11743003	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11958855	0.88[ASN][1000 genomes]
rs12517304	0.82[ASN][1000 genomes]
rs12520028	0.86[ASN][1000 genomes]
rs13178721	0.84[ASN][1000 genomes]
rs13187753	0.81[CHB][hapmap]
rs1993516	0.86[ASN][1000 genomes]
rs41236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705660	0.80[ASN][1000 genomes]
rs607821	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7704337	0.84[ASN][1000 genomes]
rs7734407	0.86[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	nsv1024203	chr5:113596392-113659935	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1021335	chr5:113599444-113659146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv537866	chr5:113599444-113659146	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv882728	chr5:113651694-113731423	Bivalent/Poised TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs554843	SRP19	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113649800-113657000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:113650800-113655000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:113653200-113657400	Enhancers	HUVEC	blood vessel
4	chr5:113653600-113654600	Weak transcription	Left Ventricle	heart
5	chr5:113653600-113658200	Weak transcription	Right Ventricle	heart
6	chr5:113653800-113654800	Weak transcription	Right Atrium	heart
7	chr5:113654000-113655400	Weak transcription	hESC Derived CD56+ Mesoderm 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