Variant report

Variant	rs55959208
Chromosome Location	chr2:114374877-114374878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1040646	0.83[ASN][1000 genomes]
rs1665302	0.86[ASN][1000 genomes]
rs1667103	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1739509	0.86[ASN][1000 genomes]
rs1964835	0.82[ASN][1000 genomes]
rs60533451	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	esv2759085	chr2:114074949-114428678	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
2	nsv428062	chr2:114251945-114428678	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	esv2757827	chr2:114253780-114428678	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
4	nsv582714	chr2:114280860-114411190	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1807730	chr2:114312991-114398343	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv821507	chr2:114322271-114376565	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA	8 gene(s)	inside rSNPs	diseases
7	esv1809766	chr2:114328505-114378566	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	esv1797539	chr2:114328505-114380229	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv961494	chr2:114358889-114375499	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv963711	chr2:114358889-114381866	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	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
12	nsv508163	chr2:114364609-114431004	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv961642	chr2:114369371-114378833	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs55959208	RPL23AP7	cis	Nerve Tibial	GTEx
rs55959208	RPL23AP7	cis	lung	GTEx
rs55959208	RPL23AP7	cis	Artery Tibial	GTEx
rs55959208	RPL23AP7	cis	Esophagus Mucosa	GTEx
rs55959208	RPL23AP7	cis	Whole Blood	GTEx
rs55959208	RPL23AP7	cis	Thyroid	GTEx
rs55959208	RPL23AP7	cis	Stomach	GTEx
rs55959208	RPL23AP7	cis	Adipose Subcutaneous	GTEx
rs55959208	RPL23AP7	cis	Skin Sun Exposed Lower leg	GTEx
rs55959208	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs55959208	RPL23AP7	cis	Artery Aorta	GTEx
rs55959208	RPL23AP7	cis	Muscle Skeletal	GTEx
rs55959208	DDX11L2	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114361800-114383000	Weak transcription	Fetal Lung	lung
2	chr2:114361800-114383000	Weak transcription	Right Ventricle	heart
3	chr2:114361800-114383600	Weak transcription	Liver	Liver
4	chr2:114361800-114383600	Weak transcription	Fetal Stomach	stomach
5	chr2:114362200-114380800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:114362200-114382800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:114362200-114383000	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:114362200-114383600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:114362600-114382800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:114362600-114383200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:114362800-114382800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:114367400-114383800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:114369800-114383000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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