Variant report

Variant	rs9481770
Chromosome Location	chr6:118539815-118539816
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11153725	0.87[MEX][hapmap]
rs12202829	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1413845	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1413846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs205915	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs205916	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2105020	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2356077	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs281869	0.96[MEX][hapmap]
rs2883849	0.87[MEX][hapmap]
rs4259282	0.85[ASN][1000 genomes]
rs58826473	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6569006	0.84[ASN][1000 genomes]
rs6936121	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7766406	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9374723	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9387565	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9398485	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
rs9481770	RSPH4A	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118533600-118541600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:118536800-118542000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:118537400-118541600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:118538000-118540000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:118539000-118540000	Enhancers	Fetal Heart	heart
6	chr6:118539000-118540000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr6:118539400-118541800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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