Variant report

Variant	rs1472498
Chromosome Location	chr1:197756149-197756150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197750889..197753652-chr1:197755989..197758239,2	MCF-7	breast:
2	chr1:197743450..197746320-chr1:197754020..197756173,2	MCF-7	breast:
3	chr1:197743241..197744801-chr1:197755993..197757752,2	K562	blood:
4	chr1:197751597..197753233-chr1:197754046..197756710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213047	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1039286	0.90[ASW][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10733088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1499594	1.00[AMR][1000 genomes]
rs1499595	1.00[AMR][1000 genomes]
rs1580811	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1747819	1.00[ASW][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1775455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2221133	1.00[AMR][1000 genomes]
rs2255086	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2477062	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2477064	0.88[AFR][1000 genomes]
rs2488399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2488407	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3933162	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4628536	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915247	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915252	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs4915571	1.00[AMR][1000 genomes]
rs6428414	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs733876	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518074	0.90[ASW][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs942437	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs953508	1.00[AMR][1000 genomes]
rs957939	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv947369	chr1:197750549-197778118	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197745200-197756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:197752400-197756200	Weak transcription	Esophagus	oesophagus
3	chr1:197753400-197756200	Weak transcription	Osteobl	bone
4	chr1:197755000-197757200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:197755000-197757200	Enhancers	HMEC	breast
6	chr1:197755000-197757400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:197755200-197757600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:197755400-197756600	Enhancers	NHDF-Ad	bronchial
9	chr1:197755600-197756600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:197755800-197757200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:197756000-197756400	Flanking Active TSS	NHEK	skin
12	chr1:197756000-197756600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:197756000-197759800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links