Variant report

Variant	rs366107
Chromosome Location	chr10:90525324-90525325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1214464	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1236939	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1368177	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1653833	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1653834	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1653835	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769694	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769695	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769696	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769698	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769699	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769701	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769702	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs184228	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs188571	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2053006	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2604963	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2604964	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2604966	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2776656	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2776657	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2776658	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2790695	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2790696	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2790697	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2790702	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs303452	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303455	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303458	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303459	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303460	0.94[CEU][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303461	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303462	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303463	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303465	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303466	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs364303	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs365263	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs372178	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs374362	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs375790	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs375842	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs376264	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs377423	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs377776	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs379756	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs381424	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs381963	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs382221	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs383115	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs386101	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs388954	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs389728	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs390152	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs391260	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs391722	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs392430	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs395231	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs396394	0.92[EUR][1000 genomes]
rs396952	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs398126	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs399949	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs400659	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs403572	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs405147	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs405854	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs406671	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs408922	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs409079	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs409330	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs410713	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs410725	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs411101	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs411713	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs412227	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs416301	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs417243	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs418276	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs419014	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs419049	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs419912	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs422360	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs422528	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs427541	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs427720	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs428425	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs430517	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs431003	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs431673	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs432202	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs434028	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434133	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs435159	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs436833	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs440103	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs442466	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs443886	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs444676	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs444764	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs447651	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs450252	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs452283	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs501040	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs515333	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs517884	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs529258	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs566053	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs814623	0.85[JPT][hapmap]
rs814625	0.85[JPT][hapmap]
rs814626	0.85[JPT][hapmap]
rs814627	0.85[JPT][hapmap]
rs814628	0.85[JPT][hapmap]
rs843782	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv1052613	chr10:90500521-90526379	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv825502	chr10:90518994-90528513	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs366107	CH25H	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90522600-90526600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:90523200-90525400	Genic enhancers	Monocytes-CD14+_RO01746	blood
3	chr10:90523600-90528000	Weak transcription	Ovary	ovary
4	chr10:90523800-90527200	Weak transcription	Hela-S3	cervix
5	chr10:90523800-90527400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr10:90523800-90527800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr10:90525200-90525600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr10:90525200-90526600	Enhancers	Primary monocytes fromperipheralblood	blood

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