Variant report

Variant	rs2039485
Chromosome Location	chr14:32353250-32353251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10130764	0.87[ASN][1000 genomes]
rs10141141	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10148852	0.81[JPT][hapmap]
rs10152018	0.80[CHD][hapmap]
rs10348	0.82[CHD][hapmap]
rs10483392	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11156717	0.85[ASN][1000 genomes]
rs1129622	0.82[CHD][hapmap]
rs12431828	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12589862	0.82[JPT][hapmap]
rs1889387	0.93[ASN][1000 genomes]
rs1953270	0.95[ASN][1000 genomes]
rs1959071	0.81[JPT][hapmap]
rs1959073	0.87[ASN][1000 genomes]
rs1959074	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1959075	0.87[ASN][1000 genomes]
rs2039484	0.99[ASN][1000 genomes]
rs2890046	0.84[ASN][1000 genomes]
rs4474604	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4981921	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4981922	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571481	0.95[ASN][1000 genomes]
rs7144599	0.95[ASN][1000 genomes]
rs7148374	0.97[ASN][1000 genomes]
rs7149538	0.95[ASN][1000 genomes]
rs7154334	0.99[ASN][1000 genomes]
rs8003195	0.89[ASN][1000 genomes]
rs8005663	0.81[JPT][hapmap]
rs8008105	0.87[EUR][1000 genomes]
rs8008192	0.95[ASN][1000 genomes]
rs8009593	0.87[EUR][1000 genomes]
rs8015328	0.81[JPT][hapmap]
rs8016004	0.87[ASN][1000 genomes]
rs8021532	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8022047	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8022995	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564180	chr14:31958566-32368934	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv564181	chr14:31958761-32363980	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv564182	chr14:32110519-32584337	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1046526	chr14:32110537-32567426	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv526200	chr14:32308511-32454372	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Brain lesion load	19010793	GWAS catalog

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32347000-32361400	Weak transcription	Right Atrium	heart
2	chr14:32349600-32355200	Enhancers	HMEC	breast
3	chr14:32349800-32355000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr14:32349800-32355000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:32349800-32355200	Enhancers	NHEK	skin
6	chr14:32349800-32356000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:32350600-32353400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:32350600-32360600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:32351400-32355400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr14:32351600-32353400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr14:32351600-32353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr14:32351600-32353600	Weak transcription	HSMM	muscle
13	chr14:32351600-32353600	Weak transcription	NH-A	brain
14	chr14:32351600-32353600	Weak transcription	NHLF	lung
15	chr14:32351600-32354000	Weak transcription	NHDF-Ad	bronchial
16	chr14:32351600-32362000	Weak transcription	Right Ventricle	heart
17	chr14:32351800-32353400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:32351800-32353400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:32351800-32353400	Weak transcription	Placenta	Placenta
20	chr14:32351800-32353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:32351800-32354000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:32351800-32354400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:32351800-32355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:32351800-32355400	Weak transcription	Osteobl	bone
25	chr14:32351800-32360600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr14:32351800-32361400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr14:32351800-32361400	Weak transcription	Left Ventricle	heart
28	chr14:32351800-32361600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr14:32351800-32362000	Weak transcription	Adipose Nuclei	Adipose
30	chr14:32351800-32362600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:32351800-32362800	Weak transcription	Spleen	Spleen
32	chr14:32352000-32354200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr14:32352000-32357800	Weak transcription	Brain Germinal Matrix	brain
34	chr14:32353200-32353800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:32353200-32353800	Enhancers	HSMMtube	muscle
36	chr14:32353200-32354600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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