Variant report

Variant	rs646698
Chromosome Location	chr9:79317722-79317723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79280437..79281078-chr9:79317445..79318438,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265488	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10869799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500952	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505034	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs509489	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs512110	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517634	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554143	0.81[EUR][1000 genomes]
rs556725	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs560094	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561970	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566584	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572737	1.00[ASN][1000 genomes]
rs591411	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594498	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611461	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615187	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618145	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620321	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620476	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620552	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620737	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625981	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs626416	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs650682	0.89[ASN][1000 genomes]
rs677913	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs680729	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680775	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018971	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7033337	0.87[EUR][1000 genomes]
rs7033978	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs646698	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79314200-79320000	Enhancers	Fetal Brain Male	brain
3	chr9:79314400-79317800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:79314400-79317800	Genic enhancers	HSMMtube	muscle
5	chr9:79314400-79318800	Enhancers	Fetal Muscle Leg	muscle
6	chr9:79314800-79318800	Enhancers	Fetal Stomach	stomach
7	chr9:79315000-79318000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr9:79315200-79319400	Weak transcription	Stomach Mucosa	stomach
9	chr9:79315200-79319600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:79315400-79318000	Weak transcription	Fetal Lung	lung
12	chr9:79315400-79319400	Weak transcription	Fetal Kidney	kidney
13	chr9:79315800-79318000	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:79315800-79318400	Weak transcription	Fetal Thymus	thymus
15	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:79316400-79319800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:79316600-79319000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:79316600-79319400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:79316600-79324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:79316800-79318000	Weak transcription	Osteobl	bone
22	chr9:79316800-79319400	Weak transcription	Brain Angular Gyrus	brain
23	chr9:79316800-79319800	Weak transcription	Brain Anterior Caudate	brain
24	chr9:79316800-79322800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:79316800-79325400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:79317200-79317800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:79317200-79318200	Strong transcription	Colon Smooth Muscle	Colon
30	chr9:79317200-79319600	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:79317400-79318000	Enhancers	HUVEC	blood vessel
32	chr9:79317400-79319800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:79317600-79318200	Weak transcription	Brain Substantia Nigra	brain
36	chr9:79317600-79318800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:79317600-79319200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr9:79317600-79319400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:79317600-79319400	Weak transcription	NHDF-Ad	bronchial
40	chr9:79317600-79320000	Weak transcription	Aorta	Aorta
41	chr9:79317600-79330800	Strong transcription	HSMM	muscle

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