Variant report

Variant	rs2376119
Chromosome Location	chr9:2418364-2418365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12000541	0.82[ASN][1000 genomes]
rs1331836	0.82[ASN][1000 genomes]
rs4741704	0.81[ASN][1000 genomes]
rs7019582	0.82[ASN][1000 genomes]
rs7023637	0.82[ASN][1000 genomes]
rs7038869	0.82[ASN][1000 genomes]
rs7041232	0.82[ASN][1000 genomes]
rs872038	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs872039	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv613128	chr9:2253678-2419538	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv892063	chr9:2291635-2419538	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv892064	chr9:2301610-2447910	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv466080	chr9:2318486-2432800	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv613131	chr9:2318486-2432800	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv531563	chr9:2324333-2501030	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1021309	chr9:2336185-2506959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv892065	chr9:2342366-2424322	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv466082	chr9:2403909-2421273	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv613133	chr9:2403909-2421273	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv1020479	chr9:2407980-2528346	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv539933	chr9:2407980-2528346	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv892067	chr9:2416895-2515607	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2376119	VLDLR	cis	Artery Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2407800-2418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:2412000-2418800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:2412200-2418800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:2412600-2420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:2412800-2418400	Weak transcription	Adipose Nuclei	Adipose
6	chr9:2412800-2418400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:2413000-2418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:2413000-2418400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:2413000-2418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:2413000-2418600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:2413000-2420400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:2413200-2418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:2413400-2418400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:2413400-2418800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:2414000-2418400	Weak transcription	Fetal Stomach	stomach
16	chr9:2414400-2418800	Weak transcription	Fetal Lung	lung
17	chr9:2414600-2418800	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:2414800-2418600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:2415200-2426800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:2415600-2418600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr9:2416000-2424400	Weak transcription	Pancreas	Pancrea
22	chr9:2416600-2423600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:2416800-2421200	Enhancers	Ovary	ovary
24	chr9:2417400-2429600	Weak transcription	Aorta	Aorta
25	chr9:2417600-2419400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr9:2417600-2420000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:2417600-2420800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:2417800-2418400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:2417800-2418800	Weak transcription	Left Ventricle	heart
30	chr9:2417800-2419200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr9:2417800-2419400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:2417800-2421200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr9:2418000-2418600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:2418000-2420400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr9:2418200-2418600	Enhancers	Brain Hippocampus Middle	brain
36	chr9:2418200-2419000	Enhancers	Brain Germinal Matrix	brain
37	chr9:2418200-2419000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr9:2418200-2419000	Enhancers	NH-A	brain
39	chr9:2418200-2419200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr9:2418200-2419200	Enhancers	Brain Anterior Caudate	brain
41	chr9:2418200-2419200	Enhancers	Fetal Brain Female	brain
42	chr9:2418200-2419400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr9:2418200-2419400	Enhancers	Brain Substantia Nigra	brain

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