Variant report

Variant	rs6759053
Chromosome Location	chr2:230993134-230993135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11893862	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052677	0.96[ASN][1000 genomes]
rs12052680	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12616682	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16826639	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16826643	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34371224	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35376505	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35490805	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35959887	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4263101	0.81[EUR][1000 genomes]
rs4277512	0.96[ASN][1000 genomes]
rs4972934	0.80[EUR][1000 genomes]
rs4972935	0.80[EUR][1000 genomes]
rs4973265	0.82[EUR][1000 genomes]
rs55982019	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58937409	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59556384	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62190338	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62190342	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62190343	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62190344	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62190347	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62190348	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6414216	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436899	0.80[EUR][1000 genomes]
rs66869073	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6705913	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715401	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743904	0.96[ASN][1000 genomes]
rs6758938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558144	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596380	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751843	chr2:230667570-230993134	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv875942	chr2:230959532-231008980	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv875943	chr2:230960946-231027162	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2830298	chr2:230988148-230995447	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6759053	POLR2A	cis	cerebellum	SCAN
rs6759053	SNORA75	cis	cerebellum	SCAN
rs6759053	ALPI	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:230989400-230993800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:230990000-230993600	Weak transcription	Placenta	Placenta
3	chr2:230990400-230993200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:230990600-230993400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:230990600-230993800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:230990800-230994200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr2:230991000-230993600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:230991600-230995800	Weak transcription	Lung	lung
9	chr2:230991800-230993400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:230991800-230993400	Enhancers	Adipose Nuclei	Adipose
11	chr2:230992000-230993200	Weak transcription	Fetal Lung	lung
12	chr2:230992000-230995800	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:230992200-230993800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:230992200-230993800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:230992200-230993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:230992200-230993800	Weak transcription	Spleen	Spleen
17	chr2:230992400-230993800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:230992800-230993800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:230992800-230993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:230992800-230993800	Weak transcription	HSMMtube	muscle
21	chr2:230992800-230999200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:230993000-230993200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:230993000-230995600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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