Variant report

Variant	rs677913
Chromosome Location	chr9:79305452-79305453
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10869799	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs500952	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505034	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512110	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs517634	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554143	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs556725	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560094	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs561970	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566584	0.89[ASN][1000 genomes]
rs572737	0.89[ASN][1000 genomes]
rs591411	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594498	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594586	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs611461	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs615187	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs618145	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620321	0.89[ASN][1000 genomes]
rs620476	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620552	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620737	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625981	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs626416	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs646698	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs650682	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680729	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs680775	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7033978	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs677913	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
2	chr9:79290400-79306000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:79302600-79305600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr9:79302600-79306600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr9:79302600-79306800	Enhancers	Fetal Intestine Large	intestine
7	chr9:79302600-79306800	Enhancers	Fetal Intestine Small	intestine
8	chr9:79302800-79306600	Weak transcription	Adipose Nuclei	Adipose
9	chr9:79303000-79305800	Weak transcription	Brain Germinal Matrix	brain
10	chr9:79303000-79306600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:79303200-79306000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:79303200-79306000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:79303200-79306200	Enhancers	HepG2	liver
14	chr9:79303400-79306800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:79303600-79305600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:79303600-79306000	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:79303600-79306000	Weak transcription	Gastric	stomach
18	chr9:79303800-79305800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:79303800-79306800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:79304000-79306400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:79304000-79306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:79304200-79306000	Weak transcription	HUVEC	blood vessel
23	chr9:79304200-79306200	Weak transcription	HSMMtube	muscle
24	chr9:79304200-79306400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:79304200-79306600	Weak transcription	Brain Substantia Nigra	brain
26	chr9:79304200-79306600	Weak transcription	NHDF-Ad	bronchial
27	chr9:79304200-79306600	Weak transcription	Osteobl	bone
28	chr9:79304200-79306800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:79304200-79306800	Weak transcription	HMEC	breast
30	chr9:79304200-79307800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:79304400-79306600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr9:79304400-79306600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:79304600-79306000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr9:79304800-79306600	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:79305000-79305800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
36	chr9:79305000-79306000	Enhancers	Brain Angular Gyrus	brain
37	chr9:79305000-79306000	Weak transcription	Fetal Thymus	thymus
38	chr9:79305000-79306600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
39	chr9:79305000-79306600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:79305000-79306800	Enhancers	Fetal Lung	lung
41	chr9:79305000-79307600	Weak transcription	Aorta	Aorta
42	chr9:79305200-79305600	Weak transcription	HSMM	muscle
43	chr9:79305200-79305800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:79305200-79305800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr9:79305200-79306200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
46	chr9:79305200-79306600	Active TSS	Brain Anterior Caudate	brain
47	chr9:79305200-79306600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr9:79305200-79306800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
49	chr9:79305200-79306800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:79305200-79307200	Enhancers	Colon Smooth Muscle	Colon

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