Variant report

Variant	rs62257007
Chromosome Location	chr3:53369590-53369591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53368645..53370641-chr3:53389075..53391767,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10433617	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10433618	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1108506	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17030934	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17234771	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17235667	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41275543	0.82[AMR][1000 genomes]
rs56654807	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59145995	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62252819	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62255989	0.85[AMR][1000 genomes]
rs62255993	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62255994	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62255999	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256000	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256003	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62256009	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256043	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256049	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256050	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256053	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256965	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256966	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256968	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256969	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257009	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257011	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257013	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257024	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6780100	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6805246	0.89[ASN][1000 genomes]
rs73080266	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73082274	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622159	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9830594	0.89[EUR][1000 genomes]
rs9830895	0.91[EUR][1000 genomes]
rs9846315	0.93[EUR][1000 genomes]
rs9850440	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876801	chr3:53325905-53467506	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv876802	chr3:53325905-53470863	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53338000-53374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:53338200-53380200	Weak transcription	Fetal Brain Male	brain
3	chr3:53346000-53373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:53346200-53378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:53346400-53370000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:53346600-53380600	Weak transcription	Spleen	Spleen
7	chr3:53347200-53371400	Weak transcription	HMEC	breast
8	chr3:53352800-53380600	Weak transcription	Esophagus	oesophagus
9	chr3:53353000-53374600	Weak transcription	Fetal Brain Female	brain
10	chr3:53353000-53380600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:53353400-53377000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:53354000-53371400	Weak transcription	NHEK	skin
13	chr3:53355400-53371600	Weak transcription	HSMMtube	muscle
14	chr3:53358200-53378800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:53358400-53380600	Weak transcription	Lung	lung
16	chr3:53358600-53370200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:53358600-53371600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:53358600-53372200	Weak transcription	Pancreas	Pancrea
19	chr3:53358800-53376200	Weak transcription	K562	blood
20	chr3:53360000-53372800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:53360000-53374000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:53360400-53376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:53360600-53380400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:53360800-53375800	Weak transcription	Aorta	Aorta
25	chr3:53360800-53380600	Weak transcription	Gastric	stomach
26	chr3:53361200-53371200	Weak transcription	Psoas Muscle	Psoas
27	chr3:53361400-53380200	Weak transcription	Colonic Mucosa	Colon
28	chr3:53361600-53379000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:53362600-53376200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:53362600-53376400	Weak transcription	Stomach Mucosa	stomach
31	chr3:53362800-53378200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:53362800-53380400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:53363200-53374000	Weak transcription	NHLF	lung
34	chr3:53363200-53375200	Weak transcription	Ovary	ovary
35	chr3:53363200-53376600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:53363200-53378400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:53363200-53380600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:53363400-53371200	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:53363400-53373000	Weak transcription	GM12878-XiMat	blood
40	chr3:53363400-53380400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:53363600-53378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:53363800-53369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:53363800-53379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:53364200-53377800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:53364400-53378600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:53364600-53372600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:53364600-53376600	Weak transcription	Right Ventricle	heart
48	chr3:53365000-53378800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:53365200-53376400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:53365200-53376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links