Variant report

Variant	rs1062964
Chromosome Location	chr1:59042388-59042389
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59009849..59013755-chr1:59040870..59045611,9	MCF-7	breast:
2	chr1:59010302..59014215-chr1:59041338..59045361,8	MCF-7	breast:
3	chr1:59042150..59043809-chr1:59165578..59167965,2	MCF-7	breast:
4	chr1:59039914..59042841-chr1:59125894..59128684,2	MCF-7	breast:
5	chr1:59039784..59042509-chr1:59074910..59077228,3	MCF-7	breast:
6	chr1:59007888..59009563-chr1:59039964..59042756,2	K562	blood:
7	chr1:59003237..59005403-chr1:59039825..59042747,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173406	Chromatin interaction
ENSG00000162601	Chromatin interaction
ENSG00000162600	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs14008	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2268943	0.83[EUR][1000 genomes]
rs338241	1.00[CEU][hapmap]
rs55731318	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs56065191	0.93[EUR][1000 genomes]
rs56381640	0.93[EUR][1000 genomes]
rs58370530	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6674248	1.00[CEU][hapmap]
rs6683669	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs72672226	0.93[EUR][1000 genomes]
rs72672238	0.93[EUR][1000 genomes]
rs72672239	0.93[EUR][1000 genomes]
rs72672249	0.93[EUR][1000 genomes]
rs72672271	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72672286	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72672292	0.83[EUR][1000 genomes]
rs72674118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72674121	1.00[EUR][1000 genomes]
rs72674127	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS 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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59038400-59043600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:59040200-59043400	Active TSS	NHEK	skin
3	chr1:59040200-59043600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:59040800-59043400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:59040800-59043400	Active TSS	Placenta Amnion	Placenta Amnion
6	chr1:59041000-59043200	Active TSS	HMEC	breast
7	chr1:59041200-59042800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:59041200-59043200	ZNF genes & repeats	GM12878-XiMat	blood
9	chr1:59041200-59044200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr1:59041400-59043000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
11	chr1:59041400-59043200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:59041400-59043200	Active TSS	Hela-S3	cervix
13	chr1:59041400-59043400	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr1:59041400-59043800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:59041400-59043800	Bivalent Enhancer	Fetal Heart	heart
16	chr1:59041600-59042400	Bivalent/Poised TSS	Fetal Lung	lung
17	chr1:59041600-59043000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:59041600-59043000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:59041600-59043200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:59041600-59043200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:59041600-59043200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
22	chr1:59041600-59043200	Bivalent/Poised TSS	Thymus	Thymus
23	chr1:59041600-59043400	Active TSS	HUVEC	blood vessel
24	chr1:59041600-59043600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr1:59041800-59042400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
26	chr1:59041800-59042400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:59041800-59042400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
28	chr1:59041800-59042600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:59041800-59042600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
30	chr1:59041800-59042600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
31	chr1:59041800-59042600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
32	chr1:59041800-59042600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr1:59041800-59042600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
34	chr1:59041800-59042600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr1:59041800-59042600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr1:59041800-59042600	Flanking Active TSS	Ovary	ovary
37	chr1:59041800-59042800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
38	chr1:59041800-59042800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
39	chr1:59041800-59042800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
40	chr1:59041800-59043000	Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:59041800-59043200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:59041800-59043200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:59041800-59043200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:59041800-59043200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:59041800-59043200	Active TSS	Gastric	stomach
46	chr1:59041800-59043200	Bivalent/Poised TSS	Osteobl	bone
47	chr1:59041800-59043600	Bivalent Enhancer	Fetal Brain Male	brain
48	chr1:59042000-59042400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:59042000-59042400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr1:59042000-59042400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links