Variant report

Variant	rs28421809
Chromosome Location	chr15:40011317-40011318
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40004259..40006236-chr15:40010388..40013115,2	MCF-7	breast:
2	chr15:39991017..39993549-chr15:40010029..40012182,2	K562	blood:
3	chr15:40011315..40014662-chr15:40074849..40076901,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10520148	0.88[AFR][1000 genomes]
rs10520149	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10520150	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1073675	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12324669	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969662	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16969663	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16969664	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16969666	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16969679	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16969680	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs16969688	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16969692	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969701	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969702	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969718	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969723	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969724	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1994380	0.85[AFR][1000 genomes]
rs2129455	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2129457	0.85[AFR][1000 genomes]
rs2171309	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28417668	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs28421798	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28457210	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28504386	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28514641	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28519658	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28568868	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28570392	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28585060	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28625134	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs28626090	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs28629181	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28657849	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28691633	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28735552	0.84[EUR][1000 genomes]
rs28785006	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4085744	0.84[AFR][1000 genomes]
rs55674415	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs55899942	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56862147	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56916119	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58878379	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs60228643	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs60613947	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7170483	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7171057	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7172138	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7172155	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7172346	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7173948	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7180740	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7181354	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7181875	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7182423	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7183462	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72727029	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72727047	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs72727060	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs72727067	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72727068	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72727070	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74008680	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs74008683	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8041266	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs937961	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs937962	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv20190	chr15:40009652-40012222	Enhancers Weak transcription	Chromatin interactive region	1 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	chr15:40001200-40011800	Weak transcription	NHDF-Ad	bronchial
2	chr15:40007000-40011800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:40008800-40011600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:40009000-40012600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:40011000-40014400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:40011000-40014800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:40011200-40012800	Enhancers	Placenta	Placenta
8	chr15:40011200-40012800	Enhancers	Osteobl	bone
9	chr15:40011200-40013200	Enhancers	NHEK	skin
10	chr15:40011200-40013400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links