Variant report

Variant	rs62266274
Chromosome Location	chr3:119780828-119780829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119774518..119780956-chr3:119811182..119816004,10	MCF-7	breast:
2	chr3:119779724..119782667-chr3:119783390..119785104,2	MCF-7	breast:
3	chr3:119776030..119778321-chr3:119778657..119781863,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10433404	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934500	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10934502	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934503	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934505	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934506	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934507	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915717	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12054090	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12108149	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629015	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12630829	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632325	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12634476	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634889	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12635018	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638973	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574154	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16830567	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1870931	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980718	0.84[ASN][1000 genomes]
rs28831519	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340737	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4624596	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4688042	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4688046	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688047	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688053	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688054	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688059	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57939147	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58863896	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60235167	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264706	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62264708	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62264714	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62264734	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264739	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264742	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264743	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264747	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264749	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266277	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62266281	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797459	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633279	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7639388	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
2	chr3:119760200-119805400	Weak transcription	HMEC	breast
3	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119768800-119792800	Weak transcription	Fetal Stomach	stomach
5	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:119769800-119784800	Weak transcription	Dnd41	blood
7	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:119771800-119781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:119771800-119783600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:119771800-119805400	Weak transcription	NHEK	skin
11	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
12	chr3:119773800-119787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:119774000-119789600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:119775400-119782600	Weak transcription	Esophagus	oesophagus
15	chr3:119775800-119784200	Weak transcription	Fetal Intestine Small	intestine
16	chr3:119775800-119790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:119775800-119796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:119775800-119797600	Weak transcription	Fetal Thymus	thymus
19	chr3:119778400-119784400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119778600-119786400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:119778800-119786000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:119778800-119787800	Weak transcription	Primary B cells from cord blood	blood
23	chr3:119778800-119791200	Weak transcription	Fetal Brain Female	brain
24	chr3:119778800-119796000	Weak transcription	NHDF-Ad	bronchial
25	chr3:119778800-119796400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:119779000-119788200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:119779200-119781200	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:119779200-119783400	Weak transcription	Fetal Heart	heart
29	chr3:119779200-119789200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:119779200-119789200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:119779200-119789200	Weak transcription	A549	lung
32	chr3:119779400-119781400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:119779400-119782200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:119779400-119783400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:119779400-119789200	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:119779400-119804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:119779400-119807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:119779600-119782200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:119779600-119782200	Weak transcription	Left Ventricle	heart
40	chr3:119779600-119782200	Weak transcription	Pancreas	Pancrea
41	chr3:119779600-119784200	Weak transcription	Psoas Muscle	Psoas
42	chr3:119779600-119786400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:119779600-119787800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:119779600-119789200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:119779600-119789600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:119779600-119789800	Weak transcription	Small Intestine	intestine
47	chr3:119779600-119793000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:119779600-119800200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:119779600-119807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:119779800-119783600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links