Variant report

Variant	rs28665952
Chromosome Location	chr15:52785041-52785042
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52783522..52785141-chr15:52819333..52821090,2	MCF-7	breast:
2	chr15:52782555..52786559-chr15:52788524..52791233,4	MCF-7	breast:
3	chr15:52782374..52785107-chr15:52859871..52862503,3	MCF-7	breast:
4	chr15:52779012..52781482-chr15:52782947..52786199,3	K562	blood:
5	chr15:52777384..52780171-chr15:52780757..52785344,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13329510	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1693516	1.00[EUR][1000 genomes]
rs1693517	1.00[EUR][1000 genomes]
rs1693519	1.00[EUR][1000 genomes]
rs1724599	1.00[EUR][1000 genomes]
rs1724600	1.00[EUR][1000 genomes]
rs1724602	1.00[EUR][1000 genomes]
rs2222656	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28401713	1.00[ASN][1000 genomes]
rs28417081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417825	1.00[EUR][1000 genomes]
rs28421476	1.00[AMR][1000 genomes]
rs28483042	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28485251	1.00[AMR][1000 genomes]
rs28485735	0.87[ASN][1000 genomes]
rs28499517	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28510975	1.00[ASN][1000 genomes]
rs28545705	1.00[ASN][1000 genomes]
rs28556791	1.00[EUR][1000 genomes]
rs28570350	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28578651	1.00[ASN][1000 genomes]
rs28581262	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613360	1.00[AMR][1000 genomes]
rs28642806	1.00[ASN][1000 genomes]
rs28663524	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28682547	1.00[EUR][1000 genomes]
rs28687913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28699673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729511	1.00[EUR][1000 genomes]
rs28761013	0.87[ASN][1000 genomes]
rs28786736	0.87[ASN][1000 genomes]
rs28795685	0.87[ASN][1000 genomes]
rs28814017	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28814321	0.87[ASN][1000 genomes]
rs28840839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28876722	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764226	0.88[ASN][1000 genomes]
rs7168981	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73412972	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73412975	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920195	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52774600-52802600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:52775200-52788400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52776400-52789000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:52776400-52796200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:52776800-52788800	Weak transcription	Osteobl	bone
6	chr15:52778600-52786200	Weak transcription	Adipose Nuclei	Adipose
7	chr15:52778600-52786200	Weak transcription	A549	lung
8	chr15:52778600-52788600	Weak transcription	Psoas Muscle	Psoas
9	chr15:52778600-52788800	Weak transcription	HSMMtube	muscle
10	chr15:52778600-52812400	Weak transcription	Right Ventricle	heart
11	chr15:52779200-52791600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:52780200-52788400	Weak transcription	Left Ventricle	heart
13	chr15:52780200-52791800	Weak transcription	Brain Angular Gyrus	brain
14	chr15:52781400-52791000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:52781600-52788400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:52781800-52795200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:52782000-52787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:52782200-52787400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:52782400-52795600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:52782600-52786200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:52782600-52788400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr15:52782600-52796200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:52782800-52785200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:52783000-52786600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:52783000-52787000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr15:52783000-52788400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:52783400-52785400	Enhancers	NHEK	skin
28	chr15:52783400-52786600	Enhancers	NHDF-Ad	bronchial
29	chr15:52783400-52786800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:52783800-52785200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:52783800-52785200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:52784000-52786200	Weak transcription	Hela-S3	cervix
33	chr15:52784000-52786200	Weak transcription	HMEC	breast
34	chr15:52784000-52788800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:52784000-52788800	Weak transcription	NHLF	lung
36	chr15:52784200-52786000	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:52784200-52786200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:52784400-52796400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:52784600-52788400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:52784600-52789600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:52784600-52792200	Enhancers	HUVEC	blood vessel
42	chr15:52784800-52786200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:52784800-52789000	Weak transcription	Brain Anterior Caudate	brain
44	chr15:52784800-52794800	Weak transcription	Colon Smooth Muscle	Colon
45	chr15:52784800-52798800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:52785000-52785400	Enhancers	Fetal Heart	heart
47	chr15:52785000-52786200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:52785000-52786200	Weak transcription	HSMM	muscle
49	chr15:52785000-52786400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:52785000-52791000	Weak transcription	Brain Substantia Nigra	brain

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