Variant report

Variant	rs1259299
Chromosome Location	chr3:120147864-120147865
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	chr3:120146209..120148260-chr3:120154802..120156441,2	MCF-7	breast:
2	chr3:120145331..120148802-chr3:120153199..120156349,3	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1259298	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1402372	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1259299	PARP9	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:120135400-120151600	Genic enhancers	Osteobl	bone
3	chr3:120136800-120148400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:120136800-120148600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:120137000-120149600	Enhancers	Rectal Smooth Muscle	rectum
6	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:120138200-120154200	Weak transcription	HMEC	breast
9	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:120138200-120169200	Weak transcription	Gastric	stomach
13	chr3:120138400-120148600	Genic enhancers	NHDF-Ad	bronchial
14	chr3:120138400-120155600	Weak transcription	Esophagus	oesophagus
15	chr3:120138600-120148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:120138800-120150600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:120139000-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:120140800-120154200	Weak transcription	Psoas Muscle	Psoas
19	chr3:120141200-120150800	Weak transcription	Brain Angular Gyrus	brain
20	chr3:120142000-120148200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:120142000-120148600	Enhancers	Aorta	Aorta
22	chr3:120142000-120149400	Genic enhancers	Fetal Stomach	stomach
23	chr3:120142000-120153600	Genic enhancers	NHLF	lung
24	chr3:120142400-120153600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:120143600-120154200	Genic enhancers	NH-A	brain
26	chr3:120143800-120149000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:120144200-120149200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:120144400-120152600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:120144800-120149200	Enhancers	Right Atrium	heart
31	chr3:120145000-120148200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:120145200-120148200	Enhancers	Left Ventricle	heart
33	chr3:120145200-120149000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:120145200-120149400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr3:120145400-120149000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:120145400-120157600	Weak transcription	Fetal Brain Female	brain
37	chr3:120145600-120149600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:120145600-120150600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:120145600-120153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:120145800-120148800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
42	chr3:120146000-120148000	Weak transcription	Brain Anterior Caudate	brain
43	chr3:120146000-120148600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:120146000-120148800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:120146000-120149600	Genic enhancers	Stomach Smooth Muscle	stomach
46	chr3:120146400-120148800	Strong transcription	Placenta	Placenta
47	chr3:120146400-120150400	Strong transcription	Fetal Intestine Large	intestine
48	chr3:120146400-120150600	Weak transcription	Fetal Kidney	kidney
49	chr3:120146400-120152400	Weak transcription	NHEK	skin
50	chr3:120146600-120148600	Strong transcription	Fetal Lung	lung

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