Variant report

Variant	rs12242499
Chromosome Location	chr10:55815852-55815853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10509004	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10825211	0.91[YRI][hapmap]
rs10825215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11004025	0.80[LWK][hapmap];0.96[YRI][hapmap]
rs11004027	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11004028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11004029	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11004030	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11004031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11004032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11004034	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11004035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11004036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11004037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11004058	0.87[EUR][1000 genomes]
rs11004060	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11591621	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11593843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11594564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11594638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595991	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11597275	0.81[CEU][hapmap]
rs11597389	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11598849	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs11599859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12243005	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244759	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12250607	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12250681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12251985	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252125	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252197	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12253866	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12255282	1.00[CEU][hapmap]
rs12256879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12256947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12257012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12257312	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258948	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16913805	0.80[CEU][hapmap]
rs16937895	1.00[CHB][hapmap]
rs16937899	1.00[CHB][hapmap]
rs17636887	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap]
rs17643506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17643564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs17644196	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs17644321	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs17711275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17711455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1911379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911401	0.82[CHB][hapmap]
rs1911402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs1911420	0.83[CHD][hapmap]
rs2135715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2610873	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2660150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2660151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2660152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2660154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2660159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28701623	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097777	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs72794984	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797006	0.87[EUR][1000 genomes]
rs72797007	0.86[EUR][1000 genomes]
rs72797008	0.86[EUR][1000 genomes]
rs72797009	0.86[EUR][1000 genomes]
rs72797010	0.86[EUR][1000 genomes]
rs72797011	0.86[EUR][1000 genomes]
rs72797012	0.88[EUR][1000 genomes]
rs72797015	0.87[EUR][1000 genomes]
rs72797020	0.84[EUR][1000 genomes]
rs72797021	0.84[EUR][1000 genomes]
rs72797022	0.85[EUR][1000 genomes]
rs72797023	0.85[EUR][1000 genomes]
rs7898152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]

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	nsv949692	chr10:55502542-55893206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv869303	chr10:55714219-55857931	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv8667	chr10:55803106-56022647	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428557	chr10:55815334-55988225	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12242499	PCDH15	cis	parietal	SCAN
rs12242499	SGMS1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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