Variant report

Variant	rs1878870
Chromosome Location	chr12:59434938-59434939
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59311843..59315228-chr12:59434167..59436634,3	MCF-7	breast:
2	chr12:59237601..59239530-chr12:59433065..59435700,2	MCF-7	breast:
3	chr12:59434389..59437372-chr12:59438954..59440734,2	MCF-7	breast:
4	chr12:59423710..59426596-chr12:59433286..59435504,3	MCF-7	breast:
5	chr12:59433661..59435709-chr12:59436125..59437780,2	MCF-7	breast:
6	chr12:59427199..59431136-chr12:59432633..59435371,3	MCF-7	breast:
7	chr12:59312784..59315143-chr12:59433489..59436442,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257443	Chromatin interaction
ENSG00000139263	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1444092	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1444094	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1444095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1444100	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1546517	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1838311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1850720	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1877258	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2120526	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2197334	1.00[AMR][1000 genomes]
rs4617627	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4760258	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7313948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7954165	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs977818	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv559048	chr12:59336737-59440659	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv559049	chr12:59359937-59436179	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59431000-59441800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:59431200-59437200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:59433200-59437400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:59433600-59435600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:59433600-59436200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:59433800-59435000	Enhancers	HUVEC	blood vessel
7	chr12:59433800-59437000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:59433800-59437200	Enhancers	HSMM	muscle
9	chr12:59434000-59435200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:59434200-59435000	Enhancers	A549	lung
11	chr12:59434200-59435200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:59434200-59435200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr12:59434200-59435200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:59434200-59435200	Enhancers	Adipose Nuclei	Adipose
15	chr12:59434200-59435200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:59434200-59435600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:59434200-59435800	Enhancers	HSMMtube	muscle
18	chr12:59434200-59436000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:59434200-59436000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:59434200-59436000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:59434200-59436000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:59434200-59436000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr12:59434200-59436200	Enhancers	Fetal Stomach	stomach
24	chr12:59434200-59437000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr12:59434200-59437200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:59434400-59435000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr12:59434400-59435000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:59434400-59435000	Enhancers	Fetal Muscle Leg	muscle
29	chr12:59434400-59435000	Enhancers	Stomach Mucosa	stomach
30	chr12:59434400-59435200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr12:59434400-59435200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr12:59434400-59435200	Flanking Active TSS	HMEC	breast
33	chr12:59434400-59435200	Flanking Active TSS	NHEK	skin
34	chr12:59434400-59435400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:59434400-59435800	Enhancers	Ovary	ovary
36	chr12:59434400-59436000	Enhancers	Fetal Lung	lung
37	chr12:59434400-59436000	Flanking Active TSS	NH-A	brain
38	chr12:59434400-59436200	Enhancers	Colon Smooth Muscle	Colon
39	chr12:59434600-59435600	Weak transcription	Pancreas	Pancrea
40	chr12:59434600-59436000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:59434800-59435000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:59434800-59435000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:59434800-59435000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:59434800-59435000	Flanking Active TSS	Fetal Kidney	kidney
45	chr12:59434800-59435200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:59434800-59435200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:59434800-59435200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:59434800-59435200	Flanking Active TSS	Hela-S3	cervix
49	chr12:59434800-59435200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr12:59434800-59435200	Flanking Active TSS	NHLF	lung

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