Variant report

Variant	rs9633743
Chromosome Location	chr10:90818777-90818778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10509563	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202955	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2000360	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2247755	1.00[JPT][hapmap]
rs2252139	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253515	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2255465	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494643	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2801533	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2801539	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841016	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841019	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2841021	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2841024	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2841025	0.81[ASN][1000 genomes]
rs2841026	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841030	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2841032	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34582012	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471339	0.85[ASN][1000 genomes]
rs7076595	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7081499	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084166	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100350	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914848	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915156	0.83[YRI][hapmap]
rs7919067	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9421696	0.82[ASN][1000 genomes]
rs9651494	0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][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	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
2	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
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv467416	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv551842	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv895880	chr10:90816060-90874029	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9633743	LDB3	cis	cerebellum	SCAN
rs9633743	KIF20B	cis	parietal	SCAN
rs9633743	HECTD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90801400-90829400	Weak transcription	Aorta	Aorta
2	chr10:90803200-90825000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:90807800-90822200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:90807800-90825000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:90808000-90823800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:90811400-90822600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:90817000-90822600	Weak transcription	Ovary	ovary
8	chr10:90817200-90818800	Weak transcription	NHLF	lung

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