Variant report

Variant	rs4849260
Chromosome Location	chr2:114449695-114449696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11677238	0.84[EUR][1000 genomes]
rs11682527	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11684486	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688799	0.83[AMR][1000 genomes]
rs11694651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448866	0.85[AMR][1000 genomes]
rs1448867	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1597245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17682500	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1975595	0.88[AMR][1000 genomes]
rs2044686	0.84[AMR][1000 genomes]
rs2418914	0.87[AMR][1000 genomes]
rs4544450	0.87[AMR][1000 genomes]
rs4849261	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849262	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4849263	0.84[AMR][1000 genomes]
rs55740782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57435814	0.81[EUR][1000 genomes]
rs6542169	0.87[AMR][1000 genomes]
rs73955046	0.83[AMR][1000 genomes]
rs7600042	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs4849260	RPL23AP7	cis	Esophagus Mucosa	GTEx
rs4849260	DDX11L2	cis	Nerve Tibial	GTEx
rs4849260	DDX11L2	cis	lung	GTEx
rs4849260	RPL23AP7	cis	lung	GTEx
rs4849260	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs4849260	DDX11L2	cis	Esophagus Muscularis	GTEx
rs4849260	DDX11L2	cis	Thyroid	GTEx
rs4849260	RP11-395L14.5	cis	Adipose Subcutaneous	GTEx
rs4849260	RPL23AP7	cis	Artery Aorta	GTEx
rs4849260	DDX11L2	cis	Esophagus Mucosa	GTEx
rs4849260	DDX11L2	cis	Heart Left Ventricle	GTEx
rs4849260	DDX11L2	cis	Muscle Skeletal	GTEx
rs4849260	DDX11L2	cis	Whole Blood	GTEx
rs4849260	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs4849260	RPL23AP7	cis	multi-tissue	Pritchard
rs4849260	RPL23AP7	cis	Whole Blood	GTEx
rs4849260	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs4849260	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs4849260	RPL23AP7	cis	Artery Tibial	GTEx
rs4849260	RPL23AP7	cis	Muscle Skeletal	GTEx
rs4849260	RPL23AP7	cis	Adipose Subcutaneous	GTEx
rs4849260	DDX11L2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114444200-114459200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:114446200-114450000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:114448600-114450200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:114448800-114459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:114449200-114450000	Enhancers	GM12878-XiMat	blood
6	chr2:114449600-114452200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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