Variant report

Variant	rs9566344
Chromosome Location	chr13:39105107-39105108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:38342917..38343939-chr13:39104444..39105331,4	MCF-7	breast:
2	chr13:38619821..38620466-chr13:39104363..39105281,2	MCF-7	breast:

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

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];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35267996	0.86[ASN][1000 genomes]
rs4470033	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61947497	0.89[ASN][1000 genomes]
rs7993470	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9315584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315585	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9315594	0.94[JPT][hapmap]
rs9315595	1.00[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs9315596	0.86[ASN][1000 genomes]
rs9532256	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9548383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548385	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548393	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9548396	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9548398	0.90[ASN][1000 genomes]
rs9548399	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9548400	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9548412	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];0.85[ASN][1000 genomes]
rs9566343	0.86[ASN][1000 genomes]
rs9566346	0.82[AFR][1000 genomes];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9566344	SPG20	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39104000-39109400	Weak transcription	Fetal Intestine Large	intestine
2	chr13:39104200-39109400	Weak transcription	Fetal Intestine Small	intestine

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