Variant report

Variant	rs1720007
Chromosome Location	chr4:8356278-8356279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1678272	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678274	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1720004	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664433	0.94[ASN][1000 genomes]
rs899489	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv470013	chr4:8315938-8377058	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv878605	chr4:8332057-8378959	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878606	chr4:8349738-8377058	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878607	chr4:8349738-8380857	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv878608	chr4:8349738-8386720	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv461219	chr4:8353829-8390646	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv593637	chr4:8353829-8390646	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1720007	TBC1D14	cis	cerebellum	SCAN
rs1720007	ACOX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8349000-8357600	Weak transcription	Fetal Heart	heart
2	chr4:8351400-8356400	Enhancers	Ovary	ovary
3	chr4:8351600-8362800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr4:8353000-8357400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:8353200-8356600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr4:8353400-8366200	Weak transcription	Aorta	Aorta
7	chr4:8353600-8356800	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:8353600-8366000	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:8353800-8357800	Enhancers	NH-A	brain
10	chr4:8354000-8357600	Weak transcription	Fetal Kidney	kidney
11	chr4:8354200-8359400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:8354200-8360000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:8354200-8366200	Weak transcription	Brain Substantia Nigra	brain
14	chr4:8354400-8357600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:8354400-8357600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:8354400-8357600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:8354400-8366000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:8354400-8366000	Weak transcription	Brain Angular Gyrus	brain
19	chr4:8354400-8367000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:8354400-8367200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:8354600-8357800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:8354600-8381000	Weak transcription	Right Atrium	heart
23	chr4:8354800-8356400	Weak transcription	HMEC	breast
24	chr4:8355000-8356600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:8355000-8358200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:8355000-8366200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:8355200-8357600	Weak transcription	Right Ventricle	heart
28	chr4:8355200-8358600	Weak transcription	Gastric	stomach
29	chr4:8355400-8357600	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:8355400-8365400	Weak transcription	Left Ventricle	heart
31	chr4:8355400-8366000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:8355800-8357000	Weak transcription	Fetal Stomach	stomach
33	chr4:8355800-8358400	Enhancers	HSMM	muscle
34	chr4:8355800-8358400	Enhancers	HSMMtube	muscle
35	chr4:8355800-8366000	Weak transcription	Lung	lung
36	chr4:8355800-8366200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:8355800-8384800	Weak transcription	Fetal Lung	lung
38	chr4:8356000-8357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:8356000-8357800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:8356000-8358600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:8356200-8357200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:8356200-8357800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:8356200-8357800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:8356200-8357800	Weak transcription	Placenta	Placenta
45	chr4:8356200-8358400	Weak transcription	Fetal Thymus	thymus
46	chr4:8356200-8358800	Enhancers	Rectal Smooth Muscle	rectum
47	chr4:8356200-8366200	Weak transcription	Thymus	Thymus

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