Variant report

Variant	rs10477009
Chromosome Location	chr5:151473561-151473562
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:151471064..151473858-chr5:151493966..151496756,2	MCF-7	breast:
2	chr5:151471420..151474359-chr5:151488636..151491340,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10079263	0.90[ASN][1000 genomes]
rs10477008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956862	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs154694	0.81[AFR][1000 genomes]
rs160036	0.83[AFR][1000 genomes]
rs160037	0.83[AFR][1000 genomes]
rs166197	0.85[AFR][1000 genomes]
rs177439	0.83[AFR][1000 genomes]
rs185252	0.85[AFR][1000 genomes]
rs1896779	0.87[AFR][1000 genomes]
rs256151	0.90[ASN][1000 genomes]
rs29849	0.83[AFR][1000 genomes]
rs29855	0.81[AFR][1000 genomes]
rs34268622	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936461	0.90[ASN][1000 genomes]
rs39806	0.81[AFR][1000 genomes]
rs524656	0.86[AFR][1000 genomes]
rs58269055	0.90[ASN][1000 genomes]
rs61322394	0.90[ASN][1000 genomes]
rs6579917	0.90[ASN][1000 genomes]
rs66860936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862288	0.90[ASN][1000 genomes]
rs6868689	0.90[ASN][1000 genomes]
rs6878015	0.90[ASN][1000 genomes]
rs6878804	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72802280	0.81[ASN][1000 genomes]
rs72802298	1.00[ASN][1000 genomes]
rs72802301	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72804303	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715309	0.90[ASN][1000 genomes]
rs7730910	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7731576	0.90[ASN][1000 genomes]
rs9324717	0.90[ASN][1000 genomes]
rs9324718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884992	0.90[ASN][1000 genomes]
rs9885356	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020899	chr5:151412785-151516788	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv508384	chr5:151438582-151487326	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv2760935	chr5:151463117-151586051	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv883039	chr5:151471642-151540888	Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv883040	chr5:151471642-151596273	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10477009	G3BP1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151471200-151475800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:151472200-151476000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:151473200-151474000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:151473200-151474000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:151473200-151474800	Enhancers	Fetal Lung	lung
6	chr5:151473400-151474400	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links