Variant report

Variant	rs34510112
Chromosome Location	chr2:113188918-113188919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13021601	0.82[EUR][1000 genomes]
rs13422242	0.80[EUR][1000 genomes]
rs6542056	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv1801285	chr2:113113618-113200081	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs34510112	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs34510112	RGPD8	cis	Thyroid	GTEx
rs34510112	RGPD8	cis	Esophagus Muscularis	GTEx
rs34510112	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs34510112	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs34510112	RGPD8	cis	Heart Left Ventricle	GTEx
rs34510112	RGPD8	cis	Muscle Skeletal	GTEx
rs34510112	RGPD8	cis	Artery Tibial	GTEx
rs34510112	RGPD8	cis	Whole Blood	GTEx
rs34510112	RGPD8	cis	Nerve Tibial	GTEx
rs34510112	ZC3H8	cis	Artery Tibial	GTEx
rs34510112	RGPD8	cis	Esophagus Mucosa	GTEx
rs34510112	RGPD8	cis	Artery Aorta	GTEx
rs34510112	RGPD8	cis	Adipose Subcutaneous	GTEx
rs34510112	RGPD8	cis	lung	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113184400-113189600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:113186600-113189000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:113187600-113189200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:113188000-113189000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:113188000-113189000	Weak transcription	HepG2	liver
6	chr2:113188000-113189600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:113188800-113189000	Enhancers	Adipose Nuclei	Adipose
8	chr2:113188800-113189000	Enhancers	HUVEC	blood vessel
9	chr2:113188800-113189200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:113188800-113189400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:113188800-113189800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:113188800-113190000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:113188800-113190000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:113188800-113190000	Enhancers	Primary T helper cells fromperipheralblood	blood

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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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