Variant report

Variant	rs9398485
Chromosome Location	chr6:118543515-118543516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11153725	0.87[MEX][hapmap]
rs12202829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1413845	0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs1413846	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17079862	0.84[AMR][1000 genomes]
rs205915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs205916	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2356077	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs281869	0.96[MEX][hapmap];0.87[TSI][hapmap]
rs2883849	0.87[MEX][hapmap]
rs4945618	0.83[AMR][1000 genomes]
rs58826473	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6936121	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs7744024	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7766406	0.85[AMR][1000 genomes]
rs9374723	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9385038	0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs9387565	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9481770	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv428153	chr6:118430517-118586974	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030089	chr6:118436482-118604516	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538427	chr6:118436482-118604516	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9398485	RSPH4A	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118542600-118544600	Weak transcription	Pancreas	Pancrea
2	chr6:118542800-118545800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:118542800-118550000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:118543000-118544400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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