Variant report

Variant	rs2587009
Chromosome Location	chr3:146260326-146260327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:146185173..146186845-chr3:146259254..146261120,2	K562	blood:
2	chr3:146234591..146236203-chr3:146259470..146262375,2	MCF-7	breast:
3	chr3:146257059..146260785-chr3:146260976..146263871,3	MCF-7	breast:
4	chr3:146234740..146236294-chr3:146259809..146262278,2	K562	blood:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1057481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079369	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13064509	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13069082	0.87[ASN][1000 genomes]
rs1373246	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443827	0.87[ASN][1000 genomes]
rs1882971	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882972	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882973	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882974	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997601	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997604	1.00[ASN][1000 genomes]
rs2120381	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165948	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587007	1.00[ASN][1000 genomes]
rs2587008	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587010	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587011	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587012	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587013	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587015	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587016	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587017	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587018	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587021	0.84[EUR][1000 genomes]
rs2587023	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2587024	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609858	0.93[ASN][1000 genomes]
rs2609860	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609861	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609864	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609865	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609867	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738905	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738906	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738907	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738910	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738911	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738912	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738915	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738916	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738918	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738920	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738923	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35214899	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35309521	0.81[ASN][1000 genomes]
rs3773510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66639703	0.84[AFR][1000 genomes]
rs67703040	0.85[ASN][1000 genomes]
rs7615988	0.90[ASN][1000 genomes]
rs9289722	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977758	0.87[ASN][1000 genomes]
rs9861142	0.90[ASN][1000 genomes]
rs9865918	0.90[ASN][1000 genomes]
rs9876886	0.93[EUR][1000 genomes];0.92[ASN][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	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146225400-146260800	Weak transcription	NH-A	brain
2	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:146247200-146260800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:146248800-146260800	Weak transcription	HSMM	muscle
6	chr3:146249400-146260800	Weak transcription	NHLF	lung
7	chr3:146250600-146260800	Weak transcription	Fetal Kidney	kidney
8	chr3:146254600-146261400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:146255000-146261000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:146255200-146260800	Weak transcription	Placenta	Placenta
11	chr3:146255400-146260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:146257000-146260800	Enhancers	HepG2	liver
13	chr3:146257200-146261000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:146257200-146261000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:146257200-146261200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:146257400-146260800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:146257400-146260800	Weak transcription	Lung	lung
18	chr3:146257400-146261200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:146257400-146261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:146257400-146261600	Weak transcription	Spleen	Spleen
21	chr3:146257400-146261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:146257600-146261400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:146257800-146260400	Enhancers	Primary T cells from cord blood	blood
24	chr3:146257800-146260600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:146257800-146260600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:146258000-146260800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:146258000-146260800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:146258000-146260800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:146258000-146263200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr3:146258400-146260600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:146258400-146263200	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr3:146258600-146260600	Enhancers	HUVEC	blood vessel
33	chr3:146258600-146261000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:146258600-146261000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr3:146258600-146262000	Active TSS	Right Atrium	heart
36	chr3:146258800-146260600	Enhancers	Stomach Mucosa	stomach
37	chr3:146258800-146260800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:146258800-146260800	Weak transcription	Fetal Heart	heart
39	chr3:146258800-146261200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr3:146258800-146262200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:146258800-146263000	Active TSS	Brain Anterior Caudate	brain
42	chr3:146258800-146263000	Active TSS	Ovary	ovary
43	chr3:146259000-146260400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:146259200-146260800	Enhancers	Osteobl	bone
45	chr3:146259200-146261000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:146259200-146262000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:146259200-146262800	Active TSS	Brain Hippocampus Middle	brain
48	chr3:146259200-146263200	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:146259200-146263200	Active TSS	Right Ventricle	heart
50	chr3:146259400-146260400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links