Variant report

Variant	rs13316480
Chromosome Location	chr3:134678040-134678041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1525015	1.00[CHB][hapmap]
rs16842308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842460	1.00[CHB][hapmap]
rs28718846	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58193970	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58195225	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61413999	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61459786	0.81[EUR][1000 genomes]
rs62270312	1.00[ASN][1000 genomes]
rs62270314	1.00[ASN][1000 genomes]
rs62270315	1.00[ASN][1000 genomes]
rs62270317	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62270318	1.00[ASN][1000 genomes]
rs62270321	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270322	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270343	0.97[EUR][1000 genomes]
rs62273061	1.00[ASN][1000 genomes]
rs66569551	0.87[AFR][1000 genomes]
rs66868541	0.83[EUR][1000 genomes]
rs6764013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810117	1.00[CHB][hapmap]
rs73214171	1.00[ASN][1000 genomes]
rs73214194	1.00[ASN][1000 genomes]
rs73218226	1.00[ASN][1000 genomes]
rs7614716	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7625747	1.00[CHB][hapmap]
rs7635428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7636773	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983401	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848835	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849294	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864852	0.83[EUR][1000 genomes]
rs9875045	0.81[EUR][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	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13316480	NMNAT3	cis	cerebellum	SCAN
rs13316480	KRAS	trans	cerebellum	SCAN
rs13316480	RAB6B	cis	parietal	SCAN
rs13316480	C3orf36	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134671000-134679400	Weak transcription	Spleen	Spleen
2	chr3:134671000-134682800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:134671000-134684600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:134671000-134693400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:134671000-134697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:134671400-134684400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:134673800-134684600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:134675200-134684600	Weak transcription	Fetal Brain Female	brain
9	chr3:134676800-134679800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:134677200-134679600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:134677400-134697400	Weak transcription	GM12878-XiMat	blood
12	chr3:134677800-134678200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:134677800-134697000	Weak transcription	Psoas Muscle	Psoas
14	chr3:134678000-134678600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links