Variant report

Variant	rs4660820
Chromosome Location	chr1:45144085-45144086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45140788..45143214-chr1:45143227..45145914,3	K562	blood:
2	chr1:45143539..45146568-chr1:45185304..45187700,3	MCF-7	breast:
3	chr1:45141963..45146217-chr1:45184774..45188907,4	MCF-7	breast:
4	chr1:45143056..45144712-chr1:45146668..45150379,3	MCF-7	breast:
5	chr1:45142356..45144412-chr1:45166029..45168004,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction
ENSG00000198520	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs3738733	0.93[AMR][1000 genomes]
rs3754421	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3768438	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs3768441	0.89[AMR][1000 genomes]
rs3850854	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs3889695	0.90[AMR][1000 genomes]
rs41524944	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4660286	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4660814	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4660819	0.90[AMR][1000 genomes]
rs72671948	0.80[AMR][1000 genomes]
rs72671949	0.80[AMR][1000 genomes]
rs72671950	0.80[AMR][1000 genomes]
rs72671962	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72671966	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72671967	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72671971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72671974	0.90[AMR][1000 genomes]
rs72671982	0.90[AMR][1000 genomes]
rs72671984	0.87[AMR][1000 genomes]
rs7532001	0.80[AMR][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:64 , 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	chr1:45140800-45145000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:45140800-45146800	Weak transcription	Esophagus	oesophagus
4	chr1:45141000-45144400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:45141000-45144800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:45141000-45144800	Enhancers	Liver	Liver
7	chr1:45141000-45144800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:45141000-45145000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:45141000-45145200	Enhancers	Adipose Nuclei	Adipose
10	chr1:45141000-45146000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:45141000-45147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:45141000-45147400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:45141000-45154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:45141000-45154800	Weak transcription	Ovary	ovary
15	chr1:45141200-45144200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:45141200-45144200	Enhancers	NHLF	lung
17	chr1:45141200-45145000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:45141200-45145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:45141200-45145800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:45141200-45146200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:45141200-45147200	Enhancers	HepG2	liver
22	chr1:45141200-45147400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:45141200-45147400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:45141200-45147800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:45141200-45164400	Weak transcription	Fetal Brain Female	brain
26	chr1:45141800-45144400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr1:45142000-45144200	Weak transcription	Left Ventricle	heart
28	chr1:45142000-45158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:45142000-45159400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:45142600-45145000	Enhancers	Brain Anterior Caudate	brain
31	chr1:45142800-45144400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:45142800-45144600	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:45142800-45151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:45143000-45144400	Enhancers	GM12878-XiMat	blood
35	chr1:45143000-45146000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:45143000-45147400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:45143000-45147400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:45143000-45147400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:45143000-45147600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:45143000-45150000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:45143200-45144400	Enhancers	Right Atrium	heart
42	chr1:45143200-45144400	Enhancers	Spleen	Spleen
43	chr1:45143200-45147200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:45143200-45147400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:45143200-45147400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:45143400-45144400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:45143400-45144600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:45143400-45145200	Weak transcription	Fetal Intestine Small	intestine
49	chr1:45143400-45147400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:45143400-45147400	Weak transcription	Small Intestine	intestine

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