Variant report

Variant	rs1555722
Chromosome Location	chr13:48458931-48458932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12867248	0.80[EUR][1000 genomes]
rs12869557	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12873785	0.96[ASN][1000 genomes]
rs17425881	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs1974039	0.96[ASN][1000 genomes]
rs2104373	0.94[ASN][1000 genomes]
rs2104374	0.93[ASN][1000 genomes]
rs2296573	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs4553498	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942710	0.94[ASN][1000 genomes]
rs6561411	0.93[ASN][1000 genomes]
rs7317860	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs7323277	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7334095	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7334463	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs7336952	0.93[ASN][1000 genomes]
rs7337766	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs7981260	0.94[ASN][1000 genomes]
rs7986369	0.97[ASN][1000 genomes]
rs7993360	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7993810	0.97[ASN][1000 genomes]
rs7994427	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7998886	0.94[ASN][1000 genomes]
rs9316346	0.92[JPT][hapmap]
rs9562779	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9567940	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9567943	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9567948	0.90[ASN][1000 genomes]
rs9591123	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9595813	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1555722	SPERT	cis	parietal	SCAN
rs1555722	ZC3H13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48449000-48464200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:48453800-48471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:48454800-48464400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:48456600-48460600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:48456600-48460600	Weak transcription	Pancreas	Pancrea
7	chr13:48457200-48478000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links