Variant report

Variant	rs12107127
Chromosome Location	chr3:19391264-19391265
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	chr3:19389760..19391334-chr3:19907874..19909391,17	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11128915	0.89[ASN][1000 genomes]
rs12108118	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632920	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12633153	0.92[ASN][1000 genomes]
rs12635216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442195	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17005851	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17005867	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28456201	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28488710	0.88[ASN][1000 genomes]
rs4425284	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56256260	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58411951	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768477	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73182727	0.89[ASN][1000 genomes]
rs73182734	0.92[ASN][1000 genomes]
rs73182739	0.93[ASN][1000 genomes]
rs73182741	0.95[ASN][1000 genomes]
rs73182745	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73182749	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73182755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73182758	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73818294	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs73819514	0.89[ASN][1000 genomes]
rs7431348	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs956380	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9812170	0.93[ASN][1000 genomes]
rs9827197	0.93[ASN][1000 genomes]
rs9827599	0.95[ASN][1000 genomes]
rs9831335	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834735	0.89[ASN][1000 genomes]
rs9839004	0.81[AFR][1000 genomes]
rs9843179	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9843569	0.97[ASN][1000 genomes]
rs9859268	0.92[ASN][1000 genomes]
rs9865301	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865551	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9865785	0.97[ASN][1000 genomes]
rs9875776	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517847	chr3:18845347-19483695	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19378400-19392400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:19382800-19391600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:19388600-19392000	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:19390000-19391600	Weak transcription	Fetal Brain Male	brain
5	chr3:19390600-19391600	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:19390600-19391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:19391200-19391400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:19391200-19392200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:19391200-19392800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:19391200-19402800	Weak transcription	Primary B cells from cord blood	blood

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