Variant report

Variant	rs4849261
Chromosome Location	chr2:114450028-114450029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10199704	0.86[MEX][hapmap]
rs10514810	1.00[ASW][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs11677238	0.84[EUR][1000 genomes]
rs11682527	0.86[EUR][1000 genomes]
rs11684486	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688799	0.83[AMR][1000 genomes]
rs11694651	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901060	0.86[MEX][hapmap]
rs12711784	0.86[MEX][hapmap]
rs13004622	0.86[MEX][hapmap]
rs13029093	0.86[MEX][hapmap]
rs1448866	0.83[AMR][1000 genomes]
rs1448867	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1584434	0.86[MEX][hapmap]
rs1597245	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17682500	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1975595	0.85[AMR][1000 genomes]
rs2044686	0.82[AMR][1000 genomes]
rs2166965	1.00[ASW][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs2305254	0.86[MEX][hapmap]
rs2418914	0.84[AMR][1000 genomes]
rs2418915	0.86[MEX][hapmap]
rs4544450	0.84[AMR][1000 genomes]
rs4849260	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849262	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4849263	0.82[AMR][1000 genomes]
rs4849269	0.86[MEX][hapmap]
rs55740782	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57435814	0.81[EUR][1000 genomes]
rs6542169	0.84[AMR][1000 genomes]
rs73955046	0.81[AMR][1000 genomes]
rs7587218	0.86[MEX][hapmap]
rs7592689	0.81[MEX][hapmap]
rs7600042	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7600550	0.86[MEX][hapmap]

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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs4849261	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs4849261	RP11-395L14.5	cis	Adipose Subcutaneous	GTEx
rs4849261	DDX11L2	cis	Artery Tibial	GTEx
rs4849261	DDX11L2	cis	Heart Left Ventricle	GTEx
rs4849261	RPL23AP7	cis	Adipose Subcutaneous	GTEx
rs4849261	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs4849261	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs4849261	RPL23AP7	cis	Muscle Skeletal	GTEx
rs4849261	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs4849261	DDX11L2	cis	Esophagus Mucosa	GTEx
rs4849261	RPL23AP7	cis	Artery Aorta	GTEx
rs4849261	DDX11L2	cis	lung	GTEx
rs4849261	DDX11L2	cis	Whole Blood	GTEx
rs4849261	DDX11L2	cis	Nerve Tibial	GTEx
rs4849261	CHCHD5	cis	cerebellum	SCAN
rs4849261	DDX11L2	cis	Stomach	GTEx
rs4849261	DDX11L2	cis	Thyroid	GTEx
rs4849261	RPL23AP7	cis	Artery Tibial	GTEx
rs4849261	MGC13005	cis	lesional skin	skin_eQTL
rs4849261	RPL23AP7	cis	lung	GTEx
rs4849261	RPL23AP7	cis	Esophagus Mucosa	GTEx
rs4849261	RPL23AP7	cis	multi-tissue	Pritchard
rs4849261	DDX11L2	cis	Muscle Skeletal	GTEx
rs4849261	DDX11L2	cis	Esophagus Muscularis	GTEx
rs4849261	RPL23AP7	cis	Whole Blood	GTEx
rs4849261	DDX11L2	cis	Artery Aorta	GTEx

Chromatin state (count:13 , 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	chr2:114448600-114450200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr2:114448800-114459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:114449600-114452200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:114449800-114452400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:114449800-114452800	Enhancers	Dnd41	blood
7	chr2:114450000-114450400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:114450000-114451800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:114450000-114452200	Enhancers	Primary B cells from cord blood	blood
10	chr2:114450000-114452200	Flanking Active TSS	GM12878-XiMat	blood
11	chr2:114450000-114452400	Enhancers	Primary hematopoietic stem cells	blood
12	chr2:114450000-114452400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:114450000-114452600	Enhancers	Primary T helper cells PMA-I stimulated	--

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