Variant report

Variant	rs66509359
Chromosome Location	chr1:45146433-45146434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45142247..45144071-chr1:45145267..45147780,2	MCF-7	breast:
2	chr1:45139936..45142593-chr1:45145834..45148217,2	MCF-7	breast:
3	chr1:45144133..45146525-chr1:45287759..45290037,2	K562	blood:
4	chr1:45146220..45150573-chr1:45184890..45188749,5	MCF-7	breast:
5	chr1:45143539..45146568-chr1:45185304..45187700,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126106	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12036630	1.00[EUR][1000 genomes]
rs1321703	1.00[EUR][1000 genomes]
rs16832186	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832188	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3738733	0.90[EUR][1000 genomes]
rs3754421	0.90[EUR][1000 genomes]
rs3768438	0.90[EUR][1000 genomes]
rs3768441	0.90[EUR][1000 genomes]
rs3850854	1.00[EUR][1000 genomes]
rs3889695	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41524944	1.00[EUR][1000 genomes]
rs4660286	1.00[EUR][1000 genomes]
rs4660814	0.90[EUR][1000 genomes]
rs4660819	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56756630	0.90[EUR][1000 genomes]
rs59834392	0.90[EUR][1000 genomes]
rs72671943	0.90[EUR][1000 genomes]
rs72671944	0.90[EUR][1000 genomes]
rs72671945	0.90[EUR][1000 genomes]
rs72671948	0.90[EUR][1000 genomes]
rs72671950	0.90[EUR][1000 genomes]
rs72671962	1.00[EUR][1000 genomes]
rs72671966	1.00[EUR][1000 genomes]
rs72671967	1.00[EUR][1000 genomes]
rs72671971	1.00[EUR][1000 genomes]
rs72671974	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671982	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671984	1.00[EUR][1000 genomes]
rs72671988	1.00[EUR][1000 genomes]
rs7532001	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7539607	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45140600-45150200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:45140800-45146800	Weak transcription	Esophagus	oesophagus
3	chr1:45141000-45147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:45141000-45147400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:45141000-45154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:45141000-45154800	Weak transcription	Ovary	ovary
7	chr1:45141200-45147200	Enhancers	HepG2	liver
8	chr1:45141200-45147400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:45141200-45147400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:45141200-45147800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45141200-45164400	Weak transcription	Fetal Brain Female	brain
12	chr1:45142000-45158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:45142000-45159400	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:45142800-45151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:45143000-45147400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:45143000-45147400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:45143000-45147400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:45143000-45147600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:45143000-45150000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:45143200-45147200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:45143200-45147400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:45143200-45147400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:45143400-45147400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:45143400-45147400	Weak transcription	Small Intestine	intestine
25	chr1:45143400-45149200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:45143600-45147400	Weak transcription	Stomach Mucosa	stomach
27	chr1:45143600-45148400	Weak transcription	NHDF-Ad	bronchial
28	chr1:45143600-45160600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:45143600-45171800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:45143800-45149200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:45143800-45149600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:45144000-45147400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:45144000-45147400	Weak transcription	Pancreas	Pancrea
34	chr1:45144000-45148600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:45144000-45150200	Weak transcription	Primary B cells from cord blood	blood
36	chr1:45144400-45149000	Weak transcription	GM12878-XiMat	blood
37	chr1:45144400-45149600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:45144400-45150200	Weak transcription	Spleen	Spleen
39	chr1:45144800-45147200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:45144800-45147800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:45145000-45147800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:45145000-45151800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:45145000-45154400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:45145000-45157000	Weak transcription	Brain Anterior Caudate	brain
45	chr1:45145200-45150400	Weak transcription	Adipose Nuclei	Adipose
46	chr1:45145600-45147600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr1:45145600-45151800	Weak transcription	Fetal Intestine Small	intestine
48	chr1:45145800-45147200	Enhancers	Liver	Liver
49	chr1:45145800-45147600	Weak transcription	Fetal Intestine Large	intestine
50	chr1:45145800-45153800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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