Variant report

Variant	rs41439350
Chromosome Location	chr20:15798483-15798484
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11697766	0.86[EUR][1000 genomes]
rs11700387	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1339256	1.00[JPT][hapmap]
rs16996498	0.90[CEU][hapmap]
rs16996594	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs16996600	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs16996618	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs16996626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17626441	0.90[CEU][hapmap]
rs17632947	0.91[CEU][hapmap]
rs17633068	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs17704936	0.91[CEU][hapmap]
rs17705904	0.91[CEU][hapmap]
rs1990396	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs55755745	0.87[EUR][1000 genomes]
rs6043534	0.90[CEU][hapmap]
rs6131725	0.82[CEU][hapmap]
rs6131746	1.00[JPT][hapmap]
rs6135552	0.81[CEU][hapmap]
rs6135553	0.82[CEU][hapmap]
rs62194752	0.91[ASN][1000 genomes]
rs7266511	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7270597	0.91[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs73097220	0.84[EUR][1000 genomes]
rs73097238	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs763659	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs763661	0.91[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv519883	chr20:15738086-15817106	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv912793	chr20:15760969-15807441	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv833929	chr20:15765372-15977337	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1847965	chr20:15766727-15807441	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv585644	chr20:15766727-15807441	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2754713	chr20:15785800-15816800	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv585645	chr20:15796051-15817106	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv458935	chr20:15796658-15816595	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv585646	chr20:15796658-15816595	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41439350	TASP1	cis	cerebellum	SCAN
rs41439350	C20orf72	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15790200-15799000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:15796000-15799000	Weak transcription	Liver	Liver
3	chr20:15798000-15798600	Enhancers	HSMM	muscle
4	chr20:15798200-15799800	Enhancers	Placenta	Placenta
5	chr20:15798200-15799800	Enhancers	HSMMtube	muscle
6	chr20:15798400-15799600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr20:15798400-15799800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:15798400-15799800	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links