Variant report

Variant	rs12059860
Chromosome Location	chr1:47284923-47284924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11211343	1.00[CEU][hapmap]
rs11211371	1.00[EUR][1000 genomes]
rs11211378	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11211379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11211380	0.85[EUR][1000 genomes]
rs11801744	1.00[CEU][hapmap]
rs12057560	1.00[CEU][hapmap]
rs12058654	0.82[YRI][hapmap]
rs12063040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073509	0.92[AFR][1000 genomes]
rs12078446	1.00[EUR][1000 genomes]
rs12090240	0.85[EUR][1000 genomes]
rs12091737	1.00[CEU][hapmap]
rs12566278	1.00[CEU][hapmap]
rs1258055	1.00[CEU][hapmap]
rs1258064	1.00[CEU][hapmap]
rs1258065	1.00[CEU][hapmap]
rs1258066	1.00[CEU][hapmap]
rs1258072	1.00[CEU][hapmap]
rs1273237	1.00[CEU][hapmap]
rs13374909	1.00[CEU][hapmap]
rs17102599	0.82[YRI][hapmap]
rs1933932	1.00[CEU][hapmap]
rs2241863	1.00[CEU][hapmap]
rs2241864	1.00[CEU][hapmap]
rs2476155	1.00[CEU][hapmap]
rs3766218	1.00[CEU][hapmap]
rs3766220	1.00[CEU][hapmap]
rs3766222	1.00[CEU][hapmap]
rs45445292	0.87[EUR][1000 genomes]
rs45528744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45562931	1.00[EUR][1000 genomes]
rs45568843	0.80[EUR][1000 genomes]
rs45580838	0.87[EUR][1000 genomes]
rs45598039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57506054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58741295	0.87[EUR][1000 genomes]
rs59598363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60332924	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs604233	1.00[CEU][hapmap]
rs604264	1.00[CEU][hapmap]
rs629412	1.00[CEU][hapmap]
rs631368	1.00[CEU][hapmap]
rs631840	1.00[CEU][hapmap]
rs636082	1.00[CEU][hapmap]
rs636122	1.00[CEU][hapmap]
rs6677350	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs669647	1.00[CEU][hapmap]
rs685862	1.00[CEU][hapmap]
rs723333	1.00[CEU][hapmap]
rs724309	1.00[CEU][hapmap]
rs72886584	1.00[EUR][1000 genomes]
rs736188	1.00[CEU][hapmap]
rs9094	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1004143	chr1:47270942-47321982	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1004246	chr1:47274901-47321982	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv947111	chr1:47277189-47308420	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Testosterone levels	22675492	GWAS catalog

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47273400-47285600	Weak transcription	Spleen	Spleen
2	chr1:47277000-47286800	Strong transcription	Esophagus	oesophagus
3	chr1:47278800-47285000	Strong transcription	Adipose Nuclei	Adipose
4	chr1:47281200-47285800	Weak transcription	Right Ventricle	heart
5	chr1:47283200-47285400	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:47284400-47285600	Weak transcription	Lung	lung
7	chr1:47284600-47285400	Weak transcription	Left Ventricle	heart

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