Variant report

Variant	rs12261856
Chromosome Location	chr10:26066590-26066591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:26065090..26066663-chr10:26068354..26071045,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10218959	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014725	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014729	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014744	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11014745	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014746	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241358	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12248775	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12251368	0.94[ASN][1000 genomes]
rs12258824	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12260808	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263936	0.94[ASN][1000 genomes]
rs13377122	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16926345	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16926353	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2437405	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2437408	0.80[ASN][1000 genomes]
rs2437409	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2442839	0.94[ASN][1000 genomes]
rs2442842	0.80[ASN][1000 genomes]
rs2442843	0.80[ASN][1000 genomes]
rs2442851	0.89[ASN][1000 genomes]
rs2505466	0.89[ASN][1000 genomes]
rs2505467	0.89[ASN][1000 genomes]
rs2505468	0.80[ASN][1000 genomes]
rs2505475	0.80[ASN][1000 genomes]
rs2505477	0.80[ASN][1000 genomes]
rs2505478	0.80[ASN][1000 genomes]
rs2505484	0.80[ASN][1000 genomes]
rs3099854	0.89[ASN][1000 genomes]
rs4335440	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57317460	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57474623	0.99[EUR][1000 genomes]
rs7070912	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089251	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093719	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100717	0.94[ASN][1000 genomes]
rs723369	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723370	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723371	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7475986	0.91[EUR][1000 genomes];0.94[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	nsv894974	chr10:26028530-26322783	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv975061	chr10:26066207-26072547	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12261856	PTCHD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26065200-26067800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:26066200-26071600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr10:26066200-26076400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr10:26066200-26082800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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