Variant report

Variant	rs42461
Chromosome Location	chr16:46802391-46802392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10468399	0.87[EUR][1000 genomes]
rs1651654	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs166161	0.86[EUR][1000 genomes]
rs16948661	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17189741	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17792604	0.87[EUR][1000 genomes]
rs2341041	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs252721	0.81[EUR][1000 genomes]
rs252722	0.81[EUR][1000 genomes]
rs28174	0.86[EUR][1000 genomes]
rs28184	0.87[EUR][1000 genomes]
rs36462	0.81[EUR][1000 genomes]
rs36464	0.87[EUR][1000 genomes]
rs36471	0.87[EUR][1000 genomes]
rs36472	0.83[EUR][1000 genomes]
rs36476	0.87[EUR][1000 genomes]
rs36481	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36483	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40163	0.87[EUR][1000 genomes]
rs40355	0.87[EUR][1000 genomes]
rs41187	0.81[EUR][1000 genomes]
rs4141491	0.86[EUR][1000 genomes]
rs415018	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs420865	0.84[EUR][1000 genomes]
rs4401068	0.89[EUR][1000 genomes]
rs4966616	0.80[EUR][1000 genomes]
rs4967393	0.87[EUR][1000 genomes]
rs57942848	0.81[EUR][1000 genomes]
rs60500837	0.80[EUR][1000 genomes]
rs66804065	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67205347	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67506574	0.81[EUR][1000 genomes]
rs67789219	0.87[EUR][1000 genomes]
rs68162608	0.81[EUR][1000 genomes]
rs698418	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs700582	0.81[EUR][1000 genomes]
rs7187475	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7190713	0.81[EUR][1000 genomes]
rs7197033	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7198951	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72816877	0.85[EUR][1000 genomes]
rs794279	0.81[EUR][1000 genomes]
rs8044443	0.81[EUR][1000 genomes]
rs8044684	0.87[EUR][1000 genomes]
rs8045353	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8046748	0.87[EUR][1000 genomes]
rs8051017	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs808432	0.81[EUR][1000 genomes]
rs808434	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs808780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs808783	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv1065253	chr16:46721805-46824369	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1059049	chr16:46721805-46859239	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv1067283	chr16:46801709-46885218	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs42461	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46791000-46823400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:46792600-46811600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:46793000-46809600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:46797600-46806000	Weak transcription	Left Ventricle	heart
5	chr16:46798000-46802600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr16:46800400-46806400	Weak transcription	Fetal Heart	heart
7	chr16:46801200-46804400	Weak transcription	GM12878-XiMat	blood
8	chr16:46802000-46803600	Enhancers	Skeletal Muscle Male	skeletal muscle

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