Variant report

Variant	rs17359910
Chromosome Location	chr4:120570769-120570770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10013852	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10021469	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10434030	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10434031	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10434032	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434033	0.86[ASN][1000 genomes]
rs10518332	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10518333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17007472	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051278	0.80[ASN][1000 genomes]
rs17355550	1.00[CEU][hapmap]
rs17357002	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17359764	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17360333	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1962195	0.86[ASN][1000 genomes]
rs2389872	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389876	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389877	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389878	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389883	0.86[ASN][1000 genomes]
rs2389884	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389891	0.86[ASN][1000 genomes]
rs2389892	0.86[ASN][1000 genomes]
rs2953290	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4146266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4833621	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58613543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58735454	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59225699	0.86[ASN][1000 genomes]
rs6534145	1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6534148	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6831062	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72922588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72922598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924305	0.86[ASN][1000 genomes]
rs72924312	0.86[ASN][1000 genomes]
rs7670921	1.00[CHB][hapmap]
rs7671191	0.86[ASN][1000 genomes]
rs7684853	0.86[ASN][1000 genomes]
rs8180145	0.80[ASN][1000 genomes]
rs8180147	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs9991735	0.86[ASN][1000 genomes]

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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17359910	SFN	trans	brain	seeQTL
rs17359910	ADAD2	trans	brain	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120568200-120573600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120568200-120573600	Weak transcription	NH-A	brain
3	chr4:120568400-120573600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:120568400-120577400	Weak transcription	Psoas Muscle	Psoas
5	chr4:120568600-120582200	Weak transcription	Fetal Brain Male	brain
6	chr4:120568800-120573200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:120568800-120573200	Weak transcription	NHLF	lung
8	chr4:120568800-120573600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:120569000-120573200	Weak transcription	Osteobl	bone
10	chr4:120569200-120573600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:120569800-120571800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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