Variant report

Variant	rs12519846
Chromosome Location	chr5:57113924-57113925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57108993..57111011-chr5:57112837..57114990,3	MCF-7	breast:
2	chr5:57112852..57115326-chr5:57117330..57119876,4	MCF-7	breast:
3	chr5:57112937..57114753-chr5:57754481..57756269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12654378	0.90[EUR][1000 genomes]
rs1347072	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1347073	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1432477	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1432480	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1432481	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16887464	0.90[EUR][1000 genomes]
rs16887469	0.90[EUR][1000 genomes]
rs1816391	0.99[ASN][1000 genomes]
rs1821211	0.89[EUR][1000 genomes]
rs1835873	0.85[ASN][1000 genomes]
rs1835875	0.86[ASN][1000 genomes]
rs1835876	0.99[ASN][1000 genomes]
rs2053013	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2215813	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2408855	0.89[EUR][1000 genomes]
rs2539732	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2539734	0.84[ASN][1000 genomes]
rs2568533	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2568534	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568535	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568536	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898030	0.99[ASN][1000 genomes]
rs2898031	0.97[ASN][1000 genomes]
rs2898032	0.89[ASN][1000 genomes]
rs34152283	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34397458	0.90[EUR][1000 genomes]
rs34711481	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35483666	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700229	0.99[ASN][1000 genomes]
rs4700230	0.99[ASN][1000 genomes]
rs62360111	0.94[ASN][1000 genomes]
rs6450440	0.93[ASN][1000 genomes]
rs6450441	0.94[ASN][1000 genomes]
rs6868222	0.89[EUR][1000 genomes]
rs6892809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757635	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701201	0.87[ASN][1000 genomes]
rs7717208	0.87[EUR][1000 genomes]
rs7721249	0.87[EUR][1000 genomes]
rs7722730	0.87[EUR][1000 genomes]
rs854025	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854026	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854027	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854030	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854032	0.85[ASN][1000 genomes]
rs854034	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887868	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57111600-57114000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr5:57111600-57114000	Enhancers	HMEC	breast
3	chr5:57111600-57114200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr5:57111600-57114200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:57111600-57114200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:57111600-57114200	Enhancers	NH-A	brain
7	chr5:57111600-57114200	Enhancers	Osteobl	bone
8	chr5:57111600-57114400	Enhancers	HSMM	muscle
9	chr5:57111600-57114600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:57112000-57114800	Enhancers	HUVEC	blood vessel
11	chr5:57112200-57114000	Enhancers	NHLF	lung
12	chr5:57112400-57114200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:57113200-57119600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:57113800-57114200	Enhancers	Fetal Lung	lung

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