Variant report

Variant	rs5002415
Chromosome Location	chr6:118281878-118281879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13198431	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13211121	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1416412	0.83[GIH][hapmap]
rs1416413	0.83[GIH][hapmap]
rs17079625	0.95[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs17821501	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2355798	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs34191954	0.86[ASN][1000 genomes]
rs34358304	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34729097	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36172496	0.86[EUR][1000 genomes]
rs4113075	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4120871	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs4945604	0.87[CEU][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs4946312	0.87[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs56292955	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914871	0.81[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs6935258	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935516	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs7744988	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9320622	0.85[GIH][hapmap]
rs9374693	0.83[AMR][1000 genomes]
rs9387527	0.83[GIH][hapmap]
rs9387528	0.83[GIH][hapmap]
rs9387532	0.87[CEU][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs9481751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489288	0.84[LWK][hapmap];0.85[YRI][hapmap]
rs9489290	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9766457	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9968789	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5002415	SLC35F1	cis	cerebellum	SCAN
rs5002415	PLN	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118273400-118282200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:118277800-118282600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:118278000-118283400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:118278200-118282000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:118278200-118283400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:118278400-118282400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:118279000-118283200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:118280000-118284400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:118281800-118282000	Enhancers	Brain Substantia Nigra	brain
10	chr6:118281800-118282200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:118281800-118284200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:118281800-118284400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links