Variant report

Variant	rs28430533
Chromosome Location	chr15:51256012-51256013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51255834..51257399-chr15:51273683..51276237,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10519289	0.83[ASN][1000 genomes]
rs11070825	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854585	0.85[ASN][1000 genomes]
rs11854729	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856129	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857981	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899397	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900973	0.82[ASN][1000 genomes]
rs12901608	0.86[ASN][1000 genomes]
rs12901860	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12902196	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903317	0.82[ASN][1000 genomes]
rs12904155	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906205	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907367	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909780	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911270	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12913094	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916334	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1438926	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16953045	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964048	0.80[ASN][1000 genomes]
rs17521467	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17521789	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521919	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599863	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17599974	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1904432	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912097	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2083254	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278559	0.83[ASN][1000 genomes]
rs2306329	0.82[ASN][1000 genomes]
rs2306333	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28366661	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28642856	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34874493	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35114758	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35134521	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35416047	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35439349	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35655196	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35684604	0.85[ASN][1000 genomes]
rs3759806	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816717	0.82[ASN][1000 genomes]
rs4134038	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58661036	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493470	0.83[ASN][1000 genomes]
rs71426066	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71471522	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71471523	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71471583	0.82[ASN][1000 genomes]
rs71471584	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71471585	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71471587	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162562	0.81[ASN][1000 genomes]
rs7165920	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166073	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7166600	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7170009	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175024	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179321	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181081	0.83[ASN][1000 genomes]
rs8032236	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032550	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032866	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034812	0.85[ASN][1000 genomes]
rs8036604	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
3	chr15:51235200-51263800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:51242800-51258200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:51243600-51256800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:51243600-51261400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:51243800-51283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:51246800-51257800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:51249800-51257000	Weak transcription	Aorta	Aorta
10	chr15:51249800-51257000	Weak transcription	Gastric	stomach
11	chr15:51249800-51257000	Weak transcription	Pancreas	Pancrea
12	chr15:51249800-51260800	Weak transcription	Esophagus	oesophagus
13	chr15:51250200-51257000	Weak transcription	Lung	lung
14	chr15:51250200-51257200	Weak transcription	Fetal Stomach	stomach
15	chr15:51250400-51264800	Weak transcription	NHEK	skin
16	chr15:51251000-51256800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:51251200-51256800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:51251200-51257000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:51251600-51257800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:51251600-51259600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr15:51251600-51261200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:51251800-51256800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:51251800-51257800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:51251800-51259400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:51251800-51260000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:51252000-51257200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:51252200-51256800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:51252200-51256800	Weak transcription	Ovary	ovary
29	chr15:51252200-51260800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:51252200-51261200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:51252200-51262400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:51252200-51263400	Weak transcription	NHLF	lung
33	chr15:51252400-51257600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:51252400-51283800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:51253200-51257200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:51253200-51257400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:51253200-51258200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:51253400-51256800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:51253400-51260600	Weak transcription	Hela-S3	cervix
40	chr15:51253400-51265600	Weak transcription	HMEC	breast
41	chr15:51253600-51261000	Weak transcription	Fetal Thymus	thymus
42	chr15:51253600-51261400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:51253600-51262200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:51253800-51256800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:51253800-51259400	Weak transcription	Osteobl	bone
46	chr15:51253800-51260400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:51253800-51262200	Weak transcription	NHDF-Ad	bronchial
48	chr15:51253800-51262400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:51253800-51262400	Weak transcription	NH-A	brain
50	chr15:51254000-51256800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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