Variant report

Variant	rs1490983
Chromosome Location	chr5:125053222-125053223
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	chr5:125052667..125055042-chr5:125057231..125059249,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10064620	0.89[ASN][1000 genomes]
rs13154003	0.99[ASN][1000 genomes]
rs1490985	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17153165	0.84[ASN][1000 genomes]
rs1873482	0.83[ASN][1000 genomes]
rs2201044	0.81[ASN][1000 genomes]
rs7709204	0.81[ASN][1000 genomes]
rs7713048	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7727138	0.94[ASN][1000 genomes]
rs7735956	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030992	chr5:124708549-125391503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv537892	chr5:124708549-125391503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv534468	chr5:124943170-125634960	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv521940	chr5:125049170-125092500	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2758014	chr5:125050863-125287909	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2759376	chr5:125050863-125287909	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:125021800-125055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:125049200-125053800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:125049200-125054400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:125049200-125055000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:125049400-125055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:125050000-125056600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:125051000-125053400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:125051000-125053600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:125051000-125057200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:125051600-125054200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:125051600-125055400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:125052000-125054000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:125052200-125053600	Enhancers	HMEC	breast
14	chr5:125052200-125053600	Enhancers	NH-A	brain
15	chr5:125052400-125055600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:125052600-125053400	Enhancers	Osteobl	bone
17	chr5:125052600-125055200	Enhancers	HepG2	liver
18	chr5:125052800-125053400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:125052800-125053600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:125053000-125053400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:125053200-125053600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:125053200-125054000	Enhancers	NHLF	lung
23	chr5:125053200-125055000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:125053200-125055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links