Variant report

Variant	rs743082
Chromosome Location	chr20:1690191-1690192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11696890	0.91[EUR][1000 genomes]
rs11697150	0.91[EUR][1000 genomes]
rs11906069	0.97[EUR][1000 genomes]
rs12480056	0.88[AFR][1000 genomes]
rs1438098	0.97[EUR][1000 genomes]
rs1438099	0.97[EUR][1000 genomes]
rs1438101	0.97[EUR][1000 genomes]
rs1595459	0.97[EUR][1000 genomes]
rs1595460	0.97[EUR][1000 genomes]
rs4602278	0.97[EUR][1000 genomes]
rs4633984	0.92[AFR][1000 genomes]
rs56198409	0.97[EUR][1000 genomes]
rs58052989	0.92[AFR][1000 genomes]
rs59719880	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6105572	0.97[EUR][1000 genomes]
rs6105573	0.97[EUR][1000 genomes]
rs6105574	0.97[EUR][1000 genomes]
rs6105579	1.00[EUR][1000 genomes]
rs6111024	0.97[EUR][1000 genomes]
rs6111031	0.97[EUR][1000 genomes]
rs6111034	0.97[EUR][1000 genomes]
rs6111041	0.97[EUR][1000 genomes]
rs6111045	0.97[EUR][1000 genomes]
rs6111046	0.97[EUR][1000 genomes]
rs6111054	0.97[EUR][1000 genomes]
rs6111055	0.97[EUR][1000 genomes]
rs6111058	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6111080	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6135782	0.83[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs6135787	0.86[YRI][hapmap];0.90[AFR][1000 genomes]
rs6135817	0.83[AFR][1000 genomes]
rs7266946	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73069323	0.95[EUR][1000 genomes]
rs73069324	0.96[EUR][1000 genomes]
rs73069326	0.96[EUR][1000 genomes]
rs73085052	0.90[EUR][1000 genomes]
rs735993	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs735994	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8116788	0.82[AFR][1000 genomes]
rs8117600	0.90[EUR][1000 genomes]

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	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1063429	chr20:1679052-1706969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1793674	chr20:1685595-1704114	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs743082	SNORD57	cis	cerebellum	SCAN
rs743082	NPM3	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1688200-1690200	Enhancers	Primary hematopoietic stem cells	blood
2	chr20:1688200-1690200	Enhancers	Thymus	Thymus
3	chr20:1688800-1693000	Weak transcription	HMEC	breast
4	chr20:1689200-1690200	Enhancers	Primary T cells from cord blood	blood
5	chr20:1689400-1698200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:1689600-1693000	Weak transcription	K562	blood

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