Variant report

Variant	rs13160125
Chromosome Location	chr5:79606636-79606637
allele	C/G
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:16)

rs_ID	r²[population]
rs10038246	0.82[ASN][1000 genomes]
rs10040789	0.81[AFR][1000 genomes]
rs10040794	0.81[AFR][1000 genomes]
rs10056190	0.87[YRI][hapmap]
rs10060692	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10064457	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1052345	0.85[JPT][hapmap]
rs12516006	0.81[ASN][1000 genomes]
rs16876315	0.85[JPT][hapmap]
rs2112151	0.81[AFR][1000 genomes]
rs2405378	0.81[ASN][1000 genomes]
rs6866850	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72763509	0.82[ASN][1000 genomes]
rs7718110	0.87[YRI][hapmap]
rs7722090	0.87[YRI][hapmap]
rs879738	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[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	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv980690	chr5:79591958-79614381	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13160125	SERINC5	cis	parietal	SCAN
rs13160125	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs13160125	MSH3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79606400-79611400	Weak transcription	iPS DF 19.11 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