Variant report

Variant	rs1900425
Chromosome Location	chr10:55638740-55638741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10740557	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10740558	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10740559	0.83[EUR][1000 genomes]
rs10763016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10763019	0.84[EUR][1000 genomes]
rs10763020	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10763021	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10763022	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10763024	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10763025	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10763027	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10763028	0.83[EUR][1000 genomes]
rs10763038	0.80[GIH][hapmap]
rs10825138	0.92[CEU][hapmap]
rs10825147	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10825148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10825149	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10825154	0.94[JPT][hapmap]
rs10825155	0.84[EUR][1000 genomes]
rs10825156	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10825157	0.92[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10825159	0.84[EUR][1000 genomes]
rs10825161	0.81[EUR][1000 genomes]
rs10825168	0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs10825185	0.88[CEU][hapmap]
rs11003893	0.92[CEU][hapmap]
rs11003898	1.00[CEU][hapmap]
rs11003902	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs11003908	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11003918	0.91[CEU][hapmap]
rs11003919	0.92[CEU][hapmap]
rs11003924	0.88[JPT][hapmap]
rs11003925	0.88[JPT][hapmap]
rs11003927	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs11003969	0.91[CEU][hapmap]
rs16937840	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1900414	0.88[JPT][hapmap]
rs1900421	0.88[CEU][hapmap]
rs1900423	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1900424	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs1900426	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap]
rs1900427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs1900437	0.81[CEU][hapmap]
rs1900444	0.87[CEU][hapmap]
rs1900449	0.83[EUR][1000 genomes]
rs1900450	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1900451	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1900453	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs1900458	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs1900459	0.87[CEU][hapmap]
rs1911427	0.86[CHB][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap]
rs1911429	0.85[GIH][hapmap]
rs2069216	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2069217	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2121525	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs2135723	0.92[CEU][hapmap]
rs2174716	0.84[CEU][hapmap]
rs2384328	0.92[CEU][hapmap]
rs2384332	0.82[EUR][1000 genomes]
rs2384333	0.83[EUR][1000 genomes]
rs2384334	0.80[EUR][1000 genomes]
rs2384340	0.92[CEU][hapmap]
rs2384343	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs2446600	0.87[CEU][hapmap]
rs2446608	0.81[CEU][hapmap]
rs2456699	0.84[CEU][hapmap]
rs2593103	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2593105	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2593106	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs2593107	0.83[GIH][hapmap]
rs2593119	0.84[EUR][1000 genomes]
rs2593120	0.92[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2593122	0.92[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2593123	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs2593124	0.83[EUR][1000 genomes]
rs2593126	0.83[JPT][hapmap]
rs2593129	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2593135	0.85[GIH][hapmap]
rs2593138	0.83[EUR][1000 genomes]
rs2593139	0.83[EUR][1000 genomes]
rs2593140	0.83[EUR][1000 genomes]
rs2610823	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2610837	0.87[CEU][hapmap];0.86[TSI][hapmap]
rs2610846	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2610857	0.83[EUR][1000 genomes]
rs2610893	0.84[CEU][hapmap]
rs2610902	0.85[CEU][hapmap]
rs2610908	0.83[CEU][hapmap]
rs2610909	0.84[CEU][hapmap]
rs2610910	0.84[CEU][hapmap]
rs2610912	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs2610919	0.92[CEU][hapmap]
rs2660173	0.85[GIH][hapmap]
rs2660178	0.88[CEU][hapmap]
rs2660183	0.85[GIH][hapmap]
rs2660184	0.85[GIH][hapmap]
rs2660197	0.84[CEU][hapmap]
rs2921912	0.92[CEU][hapmap]
rs2921922	0.86[JPT][hapmap]
rs2921923	0.82[JPT][hapmap]
rs2921924	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2921925	0.92[CEU][hapmap];1.00[TSI][hapmap]
rs2921926	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs2926391	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs2926397	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs2926398	0.83[EUR][1000 genomes]
rs2926399	0.82[EUR][1000 genomes]
rs2926404	0.88[CEU][hapmap]
rs2926410	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs2926411	0.88[JPT][hapmap]
rs41487044	0.96[ASN][1000 genomes]
rs4287256	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4364970	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4376818	1.00[CEU][hapmap]
rs4427480	0.83[EUR][1000 genomes]
rs4466737	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4478892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4478893	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4488105	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap]
rs4488106	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4586053	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs4628594	0.84[CEU][hapmap]
rs4935485	0.83[CEU][hapmap]
rs4935487	0.80[CEU][hapmap]
rs5003374	0.84[CEU][hapmap]
rs6481043	0.91[CEU][hapmap];0.89[YRI][hapmap]
rs6481045	0.88[CEU][hapmap]
rs7067725	0.83[JPT][hapmap]
rs7069577	0.84[CEU][hapmap]
rs7073930	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs7083009	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7089258	0.82[EUR][1000 genomes]
rs7089762	0.81[EUR][1000 genomes]
rs7091282	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs7095839	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7097365	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs7476991	0.84[CEU][hapmap]
rs7893789	0.92[CEU][hapmap]
rs7898068	0.88[JPT][hapmap]
rs7904289	0.92[CEU][hapmap]
rs7905665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7905801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7910658	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7920872	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1847684	chr10:55371601-55638740	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1842975	chr10:55378668-55736655	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv895429	chr10:55564355-55736655	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv550947	chr10:55634290-55662226	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1049442	chr10:55638740-55681002	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1900425	PCDH15	cis	parietal	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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