Variant report

Variant	rs28553452
Chromosome Location	chr15:72468669-72468670
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr15:72468662-72469009	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
GRAMD2	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs13329116	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329270	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28367264	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28373432	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28378260	1.00[ASW][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28379334	1.00[AMR][1000 genomes]
rs28393460	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28396234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28397237	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402155	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs28403882	1.00[AMR][1000 genomes]
rs28408067	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28428645	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28429589	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28445807	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28448787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450008	1.00[AMR][1000 genomes]
rs28450424	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28451732	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28455090	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28456991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470660	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28482979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28483934	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28504509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507982	0.81[AFR][1000 genomes]
rs28514321	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28529658	1.00[AMR][1000 genomes]
rs28536592	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28542557	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28543029	1.00[AMR][1000 genomes]
rs28547979	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28548453	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28552371	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs28569017	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28570214	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28573725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583168	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28589979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28605814	1.00[AMR][1000 genomes]
rs28625307	0.82[AFR][1000 genomes]
rs28628140	1.00[AMR][1000 genomes]
rs28628792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28634283	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28636054	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639590	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28642081	1.00[AMR][1000 genomes]
rs28643436	1.00[AMR][1000 genomes]
rs28643497	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28654176	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28654851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28654861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28657431	1.00[AMR][1000 genomes]
rs28658414	1.00[AMR][1000 genomes]
rs28660217	1.00[ASW][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28660581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28663692	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28667521	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28675378	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28701136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707151	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707565	1.00[AMR][1000 genomes]
rs28709937	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28725348	1.00[AMR][1000 genomes]
rs28727443	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28741048	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28778881	0.82[AFR][1000 genomes]
rs28786091	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28791192	1.00[AMR][1000 genomes]
rs28801155	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28808678	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28809863	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28817677	0.82[AFR][1000 genomes]
rs28824293	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28830268	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28833566	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28853032	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28872877	1.00[AMR][1000 genomes]
rs28879707	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8192372	1.00[AMR][1000 genomes]
rs9920204	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920223	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920987	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920991	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

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	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:72462000-72471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:72463600-72472200	Weak transcription	Fetal Intestine Small	intestine
4	chr15:72465000-72476200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:72466000-72470200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:72466600-72469000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:72466600-72471200	Enhancers	Placenta	Placenta
8	chr15:72466600-72472400	Enhancers	HMEC	breast
9	chr15:72466800-72476200	Weak transcription	Esophagus	oesophagus
10	chr15:72467200-72469600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:72467600-72471600	Weak transcription	Lung	lung
12	chr15:72467800-72471400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:72468000-72476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:72468200-72468800	Enhancers	Ovary	ovary
15	chr15:72468400-72469200	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:72468400-72473200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:72468400-72476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:72468600-72469000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:72468600-72469000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr15:72468600-72469000	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr15:72468600-72469200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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