Variant report

Variant	rs60469789
Chromosome Location	chr1:45145322-45145323
allele	A/T
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	chr1:45142247..45144071-chr1:45145267..45147780,2	MCF-7	breast:
3	chr1:45144133..45146525-chr1:45287759..45290037,2	K562	blood:
4	chr1:45143539..45146568-chr1:45185304..45187700,3	MCF-7	breast:
5	chr1:45141963..45146217-chr1:45184774..45188907,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117425	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1051664	0.98[ASN][1000 genomes]
rs56257701	0.97[ASN][1000 genomes]
rs58019041	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58035624	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58401148	1.00[ASN][1000 genomes]
rs58678671	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59370761	1.00[ASN][1000 genomes]
rs59764933	0.91[ASN][1000 genomes]
rs59790609	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60476008	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6429544	0.94[ASN][1000 genomes]
rs6665374	0.96[ASN][1000 genomes]
rs6667593	0.97[ASN][1000 genomes]
rs6698388	0.96[ASN][1000 genomes]
rs72671972	0.97[ASN][1000 genomes]
rs74070566	0.91[ASN][1000 genomes]
rs74070577	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7539312	0.96[ASN][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:55 , 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	chr1:45141000-45146000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:45141000-45147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:45141000-45147400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:45141000-45154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:45141000-45154800	Weak transcription	Ovary	ovary
8	chr1:45141200-45145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:45141200-45145800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:45141200-45146200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:45141200-45147200	Enhancers	HepG2	liver
12	chr1:45141200-45147400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:45141200-45147400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:45141200-45147800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:45141200-45164400	Weak transcription	Fetal Brain Female	brain
16	chr1:45142000-45158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:45142000-45159400	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:45142800-45151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:45143000-45146000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:45143000-45147400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:45143000-45147400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:45143000-45147400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:45143000-45147600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:45143000-45150000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:45143200-45147200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:45143200-45147400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:45143200-45147400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:45143400-45147400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:45143400-45147400	Weak transcription	Small Intestine	intestine
30	chr1:45143400-45149200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:45143600-45147400	Weak transcription	Stomach Mucosa	stomach
32	chr1:45143600-45148400	Weak transcription	NHDF-Ad	bronchial
33	chr1:45143600-45160600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:45143600-45171800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:45143800-45145600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:45143800-45149200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:45143800-45149600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:45144000-45147400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:45144000-45147400	Weak transcription	Pancreas	Pancrea
40	chr1:45144000-45148600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:45144000-45150200	Weak transcription	Primary B cells from cord blood	blood
42	chr1:45144400-45149000	Weak transcription	GM12878-XiMat	blood
43	chr1:45144400-45149600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:45144400-45150200	Weak transcription	Spleen	Spleen
45	chr1:45144800-45145800	Flanking Active TSS	Liver	Liver
46	chr1:45144800-45145800	Enhancers	Fetal Intestine Large	intestine
47	chr1:45144800-45147200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:45144800-45147800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:45145000-45147800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:45145000-45151800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links