Variant report

Variant	rs6414216
Chromosome Location	chr2:230992212-230992213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11893862	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052677	0.96[ASN][1000 genomes]
rs12052680	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12616682	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4263101	0.80[EUR][1000 genomes]
rs4277512	0.96[ASN][1000 genomes]
rs4973265	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55982019	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58937409	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59556384	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62190338	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705913	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714834	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715401	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743476	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743904	0.96[ASN][1000 genomes]
rs6758938	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759053	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596380	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599478	0.80[EUR][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
rs6414216	ALPI	cis	parietal	SCAN
rs6414216	SNORA75	cis	cerebellum	SCAN
rs6414216	POLR2A	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:230989400-230993800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:230989800-230992800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr2:230989800-230992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:230990000-230993600	Weak transcription	Placenta	Placenta
5	chr2:230990200-230993000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:230990400-230992800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:230990400-230992800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:230990400-230993200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:230990600-230992800	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:230990600-230993400	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:230990600-230993800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:230990800-230994200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr2:230991000-230993600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:230991600-230995800	Weak transcription	Lung	lung
15	chr2:230991800-230992800	Enhancers	HSMMtube	muscle
16	chr2:230991800-230993400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:230991800-230993400	Enhancers	Adipose Nuclei	Adipose
18	chr2:230992000-230993200	Weak transcription	Fetal Lung	lung
19	chr2:230992000-230995800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:230992200-230992400	Enhancers	Brain Angular Gyrus	brain
21	chr2:230992200-230992400	Enhancers	Small Intestine	intestine
22	chr2:230992200-230993800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:230992200-230993800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:230992200-230993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:230992200-230993800	Weak transcription	Spleen	Spleen

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