Variant report

Variant	rs66462353
Chromosome Location	chr15:56186767-56186768
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56186114..56188918-chr15:56190868..56192433,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10851599	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11071228	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11071231	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632096	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632295	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633263	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11633313	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636123	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11637576	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12102014	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12102020	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12232351	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12595359	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12595728	0.85[EUR][1000 genomes]
rs1509406	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16976600	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1912398	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1912402	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2089635	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2089636	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2102465	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288344	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28660477	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28770330	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28773028	0.86[EUR][1000 genomes]
rs28778631	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28825119	0.85[EUR][1000 genomes]
rs28863270	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56333939	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60482539	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67505007	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162435	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7175686	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176225	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7179116	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182397	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72732282	0.85[EUR][1000 genomes]
rs72734373	0.86[EUR][1000 genomes]
rs8024944	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8026172	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8029247	0.82[EUR][1000 genomes]
rs8032158	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8038646	0.86[EUR][1000 genomes]
rs8038884	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9920158	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920159	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9920184	0.81[AMR][1000 genomes];0.88[EUR][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	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv2761966	chr15:56167250-56192861	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3361699	chr15:56173709-56192307	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv569542	chr15:56185262-56210929	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66462353	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56172800-56189600	Weak transcription	Placenta	Placenta
2	chr15:56175800-56189400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:56176000-56216200	Weak transcription	Fetal Intestine Small	intestine
4	chr15:56176800-56186800	Weak transcription	NH-A	brain
5	chr15:56181800-56188800	Weak transcription	HMEC	breast
6	chr15:56185000-56189600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:56185200-56187800	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr15:56185400-56189600	Enhancers	Hela-S3	cervix
9	chr15:56186200-56186800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:56186200-56186800	Flanking Active TSS	GM12878-XiMat	blood
11	chr15:56186200-56186800	Enhancers	HSMM	muscle
12	chr15:56186200-56186800	Enhancers	HSMMtube	muscle
13	chr15:56186200-56187600	Active TSS	A549	lung
14	chr15:56186200-56188200	Active TSS	Psoas Muscle	Psoas
15	chr15:56186200-56188400	Enhancers	Primary T cells from cord blood	blood
16	chr15:56186200-56188400	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr15:56186400-56186800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:56186400-56186800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr15:56186400-56187000	Active TSS	NHDF-Ad	bronchial
20	chr15:56186400-56187600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:56186400-56187600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:56186400-56187600	Flanking Active TSS	HUVEC	blood vessel
23	chr15:56186400-56187800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:56186400-56187800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:56186400-56187800	Active TSS	Right Atrium	heart
26	chr15:56186400-56188000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:56186400-56189800	Weak transcription	Small Intestine	intestine
28	chr15:56186600-56186800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:56186600-56186800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:56186600-56186800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr15:56186600-56186800	Enhancers	Stomach Mucosa	stomach
32	chr15:56186600-56186800	Flanking Active TSS	Osteobl	bone
33	chr15:56186600-56187000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:56186600-56187000	Active TSS	Primary hematopoietic stem cells	blood
35	chr15:56186600-56187000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:56186600-56187000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:56186600-56187000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:56186600-56187000	Flanking Active TSS	NHEK	skin
39	chr15:56186600-56187800	Weak transcription	Left Ventricle	heart
40	chr15:56186600-56188000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr15:56186600-56188400	Enhancers	Dnd41	blood
42	chr15:56186600-56188800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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