Variant report

Variant	rs162871
Chromosome Location	chr3:78877509-78877510
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78875620..78878075-chr3:78879470..78882248,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10511125	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1349024	1.00[YRI][hapmap]
rs1374887	1.00[YRI][hapmap]
rs1386431	1.00[YRI][hapmap]
rs151258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162877	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17016495	1.00[CHB][hapmap]
rs17016507	1.00[CHB][hapmap]
rs17016511	1.00[CHB][hapmap]
rs179690	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1947154	1.00[YRI][hapmap]
rs2125123	1.00[CHB][hapmap]
rs329808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs329809	0.90[EUR][1000 genomes]
rs329810	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs333478	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333479	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333485	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs333489	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333497	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333498	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs333503	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333508	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773230	1.00[CHB][hapmap]
rs404130	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs410943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs448782	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs451056	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6774082	1.00[YRI][hapmap]
rs9858414	1.00[CHB][hapmap]

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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78851400-78880400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:78868000-78881600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:78873200-78879600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:78873200-78888800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:78873800-78881800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:78875000-78880600	Weak transcription	HepG2	liver
7	chr3:78875600-78884400	Weak transcription	NHDF-Ad	bronchial
8	chr3:78875600-78888800	Weak transcription	Fetal Lung	lung
9	chr3:78876200-78881600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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