Variant report

Variant	rs10060023
Chromosome Location	chr5:124304677-124304678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10041724	0.85[ASN][1000 genomes]
rs10044837	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10055285	0.90[ASN][1000 genomes]
rs10057766	0.90[ASN][1000 genomes]
rs10061263	0.80[ASN][1000 genomes]
rs10073890	0.80[ASN][1000 genomes]
rs10074013	0.80[ASN][1000 genomes]
rs10079602	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11241779	0.88[ASN][1000 genomes]
rs11743521	0.86[ASN][1000 genomes]
rs11743554	0.84[ASN][1000 genomes]
rs11951671	0.88[ASN][1000 genomes]
rs11958289	0.88[ASN][1000 genomes]
rs12109265	0.97[ASN][1000 genomes]
rs13158867	0.83[ASN][1000 genomes]
rs1374130	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17152193	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028854	0.80[ASN][1000 genomes]
rs35862376	0.88[ASN][1000 genomes]
rs36041674	0.86[ASN][1000 genomes]
rs4240384	0.97[ASN][1000 genomes]
rs4240385	0.90[ASN][1000 genomes]
rs4279337	0.80[ASN][1000 genomes]
rs4311414	0.97[ASN][1000 genomes]
rs4331894	0.97[ASN][1000 genomes]
rs4357030	0.91[ASN][1000 genomes]
rs4540171	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4836131	0.80[ASN][1000 genomes]
rs6861021	0.92[ASN][1000 genomes]
rs6861089	0.90[ASN][1000 genomes]
rs6863192	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6869863	0.86[ASN][1000 genomes]
rs6872411	0.92[ASN][1000 genomes]
rs6875187	0.97[ASN][1000 genomes]
rs6875763	0.97[ASN][1000 genomes]
rs6876036	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895658	0.86[ASN][1000 genomes]
rs73782503	0.82[ASN][1000 genomes]
rs7732618	0.97[ASN][1000 genomes]
rs9327340	0.82[ASN][1000 genomes]
rs9968605	0.97[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	nsv882822	chr5:124250018-124449375	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830474	chr5:124263628-124431299	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv599657	chr5:124284253-124330522	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10060023	ZNF608	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124299000-124306800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:124300000-124305600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:124300000-124306800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:124300000-124311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:124302000-124307800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:124302400-124307000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:124302400-124307200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:124302600-124309600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:124303000-124309600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:124304400-124309000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:124304600-124307800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links