Variant report

Variant	rs9548385
Chromosome Location	chr13:39111269-39111270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12875233	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs35267996	0.88[ASN][1000 genomes]
rs4470033	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61947497	0.90[ASN][1000 genomes]
rs7993470	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9315584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315585	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9315594	0.94[JPT][hapmap]
rs9315595	1.00[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs9315596	0.88[ASN][1000 genomes]
rs9532256	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9548383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548393	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9548396	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9548398	0.92[ASN][1000 genomes]
rs9548399	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9548400	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9548412	1.00[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs9566343	0.84[ASN][1000 genomes]
rs9566344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9566346	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548385	CSNK1A1L	cis	parietal	SCAN
rs9548385	SPG20	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39109200-39113200	Enhancers	Brain Germinal Matrix	brain
2	chr13:39109600-39112400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:39109600-39112400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:39110800-39113000	Enhancers	Fetal Brain Female	brain
5	chr13:39111000-39111800	Enhancers	Fetal Brain Male	brain

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