Variant report

Variant	rs1900458
Chromosome Location	chr10:55717494-55717495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 176 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs10740557	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10740558	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10740559	0.89[EUR][1000 genomes]
rs10740560	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10763016	0.85[CEU][hapmap]
rs10763019	0.88[EUR][1000 genomes]
rs10763020	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10763021	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10763022	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs10763024	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10763025	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10763027	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10763028	0.90[EUR][1000 genomes]
rs10763038	0.82[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs10825138	0.96[CEU][hapmap]
rs10825148	0.86[CEU][hapmap]
rs10825155	0.88[EUR][1000 genomes]
rs10825156	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10825157	0.96[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10825159	0.88[EUR][1000 genomes]
rs10825161	0.89[EUR][1000 genomes]
rs10825185	1.00[CEU][hapmap]
rs11003893	0.96[CEU][hapmap]
rs11003898	0.88[CEU][hapmap]
rs11003902	0.88[CEU][hapmap]
rs11003916	0.85[JPT][hapmap]
rs11003918	0.95[CEU][hapmap]
rs11003919	0.96[CEU][hapmap]
rs11003921	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11003968	0.88[CHD][hapmap]
rs11003969	1.00[CEU][hapmap]
rs11003977	0.88[CHD][hapmap]
rs12570313	0.98[ASN][1000 genomes]
rs12571668	0.97[ASN][1000 genomes]
rs12571882	0.88[ASN][1000 genomes]
rs12572470	0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[ASN][1000 genomes]
rs16937813	0.85[JPT][hapmap]
rs1900421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900422	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1900423	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1900424	0.88[CEU][hapmap]
rs1900425	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs1900426	0.88[CEU][hapmap]
rs1900427	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs1900444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1900446	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1900449	0.90[EUR][1000 genomes]
rs1900450	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1900451	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1900453	0.96[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs1900459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911420	0.83[CEU][hapmap]
rs1911427	0.92[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs1911429	0.87[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap]
rs1911430	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2121525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135717	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2135718	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs2135723	0.96[CEU][hapmap]
rs2166620	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166621	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2166627	0.82[EUR][1000 genomes]
rs2166628	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2174716	0.96[CEU][hapmap]
rs2246768	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2384327	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2384328	0.96[CEU][hapmap]
rs2384332	0.89[EUR][1000 genomes]
rs2384333	0.90[EUR][1000 genomes]
rs2384334	0.88[EUR][1000 genomes]
rs2384340	0.96[CEU][hapmap];1.00[MEX][hapmap]
rs2384343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2446600	0.91[CEU][hapmap]
rs2446608	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2446609	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2446610	0.81[ASN][1000 genomes]
rs2456699	0.88[CEU][hapmap]
rs2456701	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2593103	0.96[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs2593105	0.96[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs2593106	0.96[CEU][hapmap]
rs2593107	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2593119	0.80[CEU][hapmap];0.89[EUR][1000 genomes]
rs2593120	0.96[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2593122	0.96[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2593123	0.96[CEU][hapmap]
rs2593124	0.89[EUR][1000 genomes]
rs2593129	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2593131	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2593133	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2593135	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap]
rs2593136	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2593138	0.89[EUR][1000 genomes]
rs2593139	0.90[EUR][1000 genomes]
rs2593140	0.90[EUR][1000 genomes]
rs2610823	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2610837	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2610857	0.90[EUR][1000 genomes]
rs2610874	0.84[CEU][hapmap]
rs2610875	0.83[CHD][hapmap]
rs2610893	0.87[CEU][hapmap]
rs2610899	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2610902	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2610906	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2610908	0.91[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs2610909	0.88[CEU][hapmap]
rs2610910	0.88[CEU][hapmap]
rs2610912	0.96[CEU][hapmap]
rs2610919	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2660172	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2660173	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs2660178	0.92[CEU][hapmap]
rs2660183	0.81[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap]
rs2660184	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap]
rs2660186	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2660188	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2660190	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2660192	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2660197	0.88[CEU][hapmap]
rs2921912	0.96[CEU][hapmap]
rs2921924	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2921925	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2921926	0.96[CEU][hapmap]
rs2926391	0.96[CEU][hapmap]
rs2926396	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2926397	0.96[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs2926398	0.90[EUR][1000 genomes]
rs2926399	0.89[EUR][1000 genomes]
rs2926404	0.92[CEU][hapmap]
rs2926408	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926410	0.92[CEU][hapmap]
rs4287256	0.88[CEU][hapmap]
rs4364970	0.88[CEU][hapmap]
rs4376818	0.88[CEU][hapmap]
rs4427480	0.90[EUR][1000 genomes]
rs4466737	0.88[CEU][hapmap]
rs4478892	0.88[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs4478893	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs4488105	0.87[CEU][hapmap]
rs4488106	0.87[CEU][hapmap]
rs4586053	0.88[CEU][hapmap]
rs4935485	0.96[CEU][hapmap]
rs4935487	0.92[CEU][hapmap]
rs5003374	0.96[CEU][hapmap]
rs6481043	0.96[CEU][hapmap]
rs6481045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069577	0.96[CEU][hapmap]
rs7070828	0.86[CEU][hapmap]
rs7071158	0.85[EUR][1000 genomes]
rs7073930	0.88[CEU][hapmap]
rs7087311	0.83[EUR][1000 genomes]
rs7089258	0.90[EUR][1000 genomes]
rs7089762	0.89[EUR][1000 genomes]
rs7091282	0.88[CEU][hapmap]
rs7093596	0.86[EUR][1000 genomes]
rs7095839	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7097365	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs7476991	0.88[CEU][hapmap]
rs7893789	0.96[CEU][hapmap]
rs7899816	0.80[ASN][1000 genomes]
rs7904289	0.96[CEU][hapmap]
rs7905665	0.88[CEU][hapmap]
rs7905801	0.88[CEU][hapmap]
rs7910658	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7911482	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7912992	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915856	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920872	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv895430	chr10:55645953-55736655	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1052939	chr10:55654719-55769239	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv467213	chr10:55662089-55725234	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv550949	chr10:55662089-55725234	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv869303	chr10:55714219-55857931	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1900458	PCDH15	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:55714600-55718400	Enhancers	HepG2	liver
2	chr10:55715600-55717600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr10:55716600-55718200	Enhancers	Brain Hippocampus Middle	brain
4	chr10:55716800-55718000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr10:55717000-55718400	Enhancers	Brain Substantia Nigra	brain

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