Variant report

Variant	rs2053211
Chromosome Location	chr3:143774592-143774593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1075113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935505	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710441	0.87[GIH][hapmap];0.91[MEX][hapmap]
rs1354495	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs1370029	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs1504600	0.87[GIH][hapmap]
rs1530479	0.83[EUR][1000 genomes]
rs1583550	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs1595211	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs1898265	0.81[EUR][1000 genomes]
rs2221411	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs34200306	0.82[AFR][1000 genomes]
rs34379944	0.81[EUR][1000 genomes]
rs35885310	0.81[EUR][1000 genomes]
rs4431106	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs56196484	0.81[EUR][1000 genomes]
rs6767811	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6782558	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6803148	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs723490	0.87[GIH][hapmap];0.91[MEX][hapmap]
rs7631704	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs7643341	0.86[AMR][1000 genomes]
rs920968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683376	0.87[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1010117	chr3:143750590-144093775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv536748	chr3:143750590-144093775	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877569	chr3:143762420-143825439	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2053211	HPS3	cis	cerebellum	SCAN
rs2053211	C3orf58	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143772200-143775600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:143772400-143775400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:143773000-143775000	Weak transcription	Brain Anterior Caudate	brain
4	chr3:143773000-143775200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:143773000-143775600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:143773000-143775600	Enhancers	HSMM	muscle
7	chr3:143773000-143778800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:143773200-143774800	Weak transcription	HSMMtube	muscle
9	chr3:143773200-143775200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:143773400-143775200	Enhancers	Osteobl	bone
11	chr3:143773800-143774800	Enhancers	Fetal Heart	heart
12	chr3:143773800-143775000	Enhancers	Liver	Liver
13	chr3:143773800-143775200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:143774000-143775000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:143774000-143775200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:143774000-143775200	Enhancers	NHEK	skin
17	chr3:143774200-143774600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:143774200-143774600	Enhancers	Aorta	Aorta
19	chr3:143774200-143774600	Enhancers	NHDF-Ad	bronchial
20	chr3:143774200-143774800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:143774200-143775000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:143774200-143775000	Enhancers	HMEC	breast
23	chr3:143774200-143775000	Enhancers	NH-A	brain
24	chr3:143774200-143775200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:143774200-143775200	Enhancers	NHLF	lung

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