Variant report

Variant	rs35248489
Chromosome Location	chr5:124393115-124393116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:124385684..124387313-chr5:124391971..124393955,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10060665	0.82[EUR][1000 genomes]
rs10455044	1.00[ASN][1000 genomes]
rs12152877	1.00[ASN][1000 genomes]
rs13156065	1.00[ASN][1000 genomes]
rs13156954	0.95[EUR][1000 genomes]
rs13166517	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13167251	1.00[ASN][1000 genomes]
rs13167636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13170418	1.00[ASN][1000 genomes]
rs13171701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13177504	1.00[ASN][1000 genomes]
rs13178310	1.00[ASN][1000 genomes]
rs13179795	1.00[ASN][1000 genomes]
rs13181069	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185999	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33997957	1.00[ASN][1000 genomes]
rs34190797	1.00[ASN][1000 genomes]
rs34285348	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34735920	1.00[ASN][1000 genomes]
rs34881137	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34886855	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34990521	1.00[ASN][1000 genomes]
rs35129313	1.00[ASN][1000 genomes]
rs35456753	1.00[ASN][1000 genomes]
rs35655256	1.00[ASN][1000 genomes]
rs35728314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35761814	1.00[ASN][1000 genomes]
rs35967749	1.00[ASN][1000 genomes]
rs35993487	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35996109	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36056892	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36109016	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4342331	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4836143	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57154044	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58039939	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71576805	1.00[ASN][1000 genomes]
rs71576807	1.00[ASN][1000 genomes]
rs71576809	1.00[ASN][1000 genomes]
rs71576810	1.00[ASN][1000 genomes]
rs71594396	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71594399	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9686495	0.83[EUR][1000 genomes];1.00[ASN][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	nsv882822	chr5:124250018-124449375	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830474	chr5:124263628-124431299	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv4984	chr5:124377028-124401500	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv830475	chr5:124387292-124550256	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124382800-124394200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:124382800-124394200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:124388400-124396400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr5:124388400-124396400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:124388600-124395000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:124389600-124396200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:124390600-124396400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:124390800-124395400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:124391000-124393200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr5:124391200-124396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr5:124391600-124396000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr5:124391600-124396200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:124391600-124398000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:124391800-124396400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:124392000-124395800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr5:124392200-124393400	Enhancers	Fetal Stomach	stomach
17	chr5:124392200-124394000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr5:124392200-124394200	Enhancers	Brain Hippocampus Middle	brain
19	chr5:124392200-124394600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:124392200-124395600	Enhancers	HMEC	breast
21	chr5:124392200-124395600	Enhancers	Osteobl	bone
22	chr5:124392200-124396000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr5:124392200-124396400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:124392400-124393200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:124392400-124393200	Enhancers	Fetal Thymus	thymus
26	chr5:124392400-124394000	Enhancers	Fetal Lung	lung
27	chr5:124392400-124394400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:124392400-124394600	Enhancers	Brain Substantia Nigra	brain
29	chr5:124392400-124395000	Enhancers	Fetal Brain Female	brain
30	chr5:124392400-124395200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:124392400-124395200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr5:124392400-124395400	Enhancers	Brain Germinal Matrix	brain
33	chr5:124392400-124395600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:124392400-124395600	Enhancers	Fetal Kidney	kidney
35	chr5:124392400-124396000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:124392600-124393800	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:124392600-124394200	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:124392600-124394400	Enhancers	Fetal Brain Male	brain
39	chr5:124392600-124394800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:124392600-124395600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:124392800-124393200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:124392800-124393800	Weak transcription	Brain Angular Gyrus	brain
43	chr5:124392800-124393800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:124392800-124393800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:124392800-124394200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:124392800-124394600	Enhancers	Adipose Nuclei	Adipose
47	chr5:124393000-124393200	Flanking Active TSS	NHEK	skin
48	chr5:124393000-124394000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:124393000-124394000	Weak transcription	Right Atrium	heart
50	chr5:124393000-124394200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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