Variant report

Variant	rs1520879
Chromosome Location	chr3:120190220-120190221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120189185..120191313-chr3:120225259..120226793,2	MCF-7	breast:
2	chr3:120189073..120191673-chr3:120312658..120315180,2	MCF-7	breast:
3	chr3:120185144..120187635-chr3:120188543..120191304,2	MCF-7	breast:
4	chr3:120176936..120179365-chr3:120189177..120190787,2	K562	blood:

Variant related genes	Relation type
ENSG00000065518	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1520877	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1520880	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55850616	1.00[EUR][1000 genomes]
rs55893937	1.00[EUR][1000 genomes]
rs57460775	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72958801	1.00[EUR][1000 genomes]
rs72960832	0.86[AFR][1000 genomes]
rs7637904	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649619	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9289145	1.00[EUR][1000 genomes]
rs9843734	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9849292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854846	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9868131	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120170400-120190800	Weak transcription	Aorta	Aorta
2	chr3:120186000-120195000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr3:120186600-120193800	Enhancers	NHDF-Ad	bronchial
4	chr3:120186600-120195000	Enhancers	Placenta	Placenta
5	chr3:120186800-120191200	Enhancers	Fetal Heart	heart
6	chr3:120187000-120191000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:120187400-120191000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:120187400-120191000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:120187400-120191400	Enhancers	HMEC	breast
10	chr3:120187400-120193200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:120187400-120193800	Enhancers	HSMM	muscle
12	chr3:120187600-120190600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:120187600-120191000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:120187800-120191400	Enhancers	NH-A	brain
15	chr3:120187800-120193600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:120187800-120193800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:120188200-120191000	Enhancers	Colon Smooth Muscle	Colon
18	chr3:120188200-120191200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:120188400-120191000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:120188400-120192000	Enhancers	NHLF	lung
21	chr3:120188600-120190400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:120188600-120190800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:120188600-120190800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:120188600-120191200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:120188800-120191000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:120189000-120190600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:120189000-120190800	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:120189000-120190800	Weak transcription	Hela-S3	cervix
29	chr3:120189000-120191200	Enhancers	A549	lung
30	chr3:120189200-120190800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:120189200-120191000	Enhancers	NHEK	skin
32	chr3:120189200-120191400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:120189200-120194000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:120189200-120194600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:120189200-120194800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:120189400-120191800	Enhancers	HSMMtube	muscle
37	chr3:120190000-120190800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:120190000-120190800	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:120190000-120191800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:120190000-120192200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:120190000-120193400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:120190000-120196200	Weak transcription	Left Ventricle	heart
43	chr3:120190200-120190400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:120190200-120190400	Enhancers	Osteobl	bone
45	chr3:120190200-120190800	Enhancers	Stomach Smooth Muscle	stomach
46	chr3:120190200-120193200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:120190200-120194600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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