Variant report

Variant	rs454078
Chromosome Location	chr2:113888793-113888794
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113888649..113891490-chr2:113893231..113895464,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11677397	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs128964	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13011842	1.00[JPT][hapmap]
rs13030546	1.00[JPT][hapmap]
rs16065	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1630153	0.83[CEU][hapmap]
rs1794065	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1794067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1794068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2234676	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2234677	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2234678	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2234679	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2853628	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087270	1.00[YRI][hapmap]
rs3087271	0.86[CEU][hapmap]
rs315927	0.83[CEU][hapmap]
rs315931	0.82[CEU][hapmap]
rs315936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392503	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs396201	1.00[YRI][hapmap]
rs408392	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs419598	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs423904	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4251967	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251968	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251969	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251970	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251974	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251975	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251976	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251977	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251978	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251979	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4251980	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4251981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251983	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251984	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251985	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4251986	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs431726	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432014	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434792	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440286	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs442710	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs444413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs446433	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs447713	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs448341	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451578	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495282	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs495410	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs579543	0.84[AMR][1000 genomes]
rs598859	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878972	0.85[AMR][1000 genomes];0.92[EUR][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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1013513	chr2:113876914-113893482	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113876000-113896200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:113882600-113890000	Weak transcription	Lung	lung
3	chr2:113882800-113889200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113882800-113891200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:113883400-113891000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:113885000-113890400	Strong transcription	NHEK	skin
7	chr2:113885200-113892200	Strong transcription	Esophagus	oesophagus
8	chr2:113885400-113890400	Weak transcription	Fetal Thymus	thymus
9	chr2:113885800-113891000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:113885800-113896200	Weak transcription	Placenta	Placenta
11	chr2:113886200-113891200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:113886400-113889600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:113886800-113888800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
14	chr2:113887200-113889200	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:113887400-113888800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:113887400-113889400	Genic enhancers	Liver	Liver
17	chr2:113887400-113889400	Genic enhancers	HepG2	liver
18	chr2:113887400-113890800	Strong transcription	Gastric	stomach
19	chr2:113887400-113890800	Strong transcription	Spleen	Spleen
20	chr2:113887800-113888800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:113888600-113889200	Strong transcription	HMEC	breast
22	chr2:113888600-113892000	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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