Variant report

Variant	rs4244569
Chromosome Location	chr15:39705721-39705722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39704919..39707647-chr20:52293554..52295684,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11070202	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855573	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148895	0.87[EUR][1000 genomes]
rs12906753	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907239	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244570	0.81[EUR][1000 genomes]
rs4306475	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344715	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4405525	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4417529	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4522393	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4556763	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4622487	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4923826	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924354	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55638424	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57817952	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58084121	0.82[EUR][1000 genomes]
rs59238363	0.96[EUR][1000 genomes]
rs6492889	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026812	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8029673	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8038785	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1047032	chr15:39679896-39706685	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4244569	RP11-624L4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39700000-39707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:39702400-39706000	Enhancers	HMEC	breast
3	chr15:39702600-39706000	Enhancers	NHEK	skin
4	chr15:39702800-39706200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:39703200-39708000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:39703200-39708600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:39703400-39706600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:39703800-39706400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:39703800-39706800	Weak transcription	HepG2	liver
10	chr15:39704000-39706600	Enhancers	GM12878-XiMat	blood
11	chr15:39704200-39705800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:39704200-39708400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr15:39704200-39718800	Weak transcription	Thymus	Thymus
14	chr15:39704400-39705800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:39704600-39707200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:39705000-39706000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:39705000-39707200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:39705400-39706800	Enhancers	NHDF-Ad	bronchial
19	chr15:39705400-39708600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:39705600-39708800	Enhancers	Monocytes-CD14+_RO01746	blood

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