Variant report

Variant	rs28654861
Chromosome Location	chr15:72398746-72398747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72394985..72397263-chr15:72398518..72401032,2	MCF-7	breast:
2	chr15:72398664..72401840-chr15:72410348..72413852,3	K562	blood:
3	chr15:72398478..72400917-chr15:72408968..72411115,2	MCF-7	breast:
4	chr15:72398211..72399947-chr15:72411763..72414182,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066933	Chromatin interaction
ENSG00000166192	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

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[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]
rs28397783	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28403882	1.00[AMR][1000 genomes]
rs28408067	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28409017	0.82[AFR][1000 genomes]
rs28409864	1.00[AMR][1000 genomes]
rs28413902	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28416103	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]
rs28430988	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]
rs28449356	0.82[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]
rs28485920	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28501562	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28504509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28504990	1.00[AMR][1000 genomes]
rs28507982	0.81[AFR][1000 genomes]
rs28514321	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28515972	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[AMR][1000 genomes]
rs28553452	1.00[AFR][1000 genomes];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]
rs28578220	0.82[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]
rs28599944	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]
rs28630701	0.82[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]
rs28657431	1.00[AMR][1000 genomes]
rs28658414	1.00[AMR][1000 genomes]
rs28660217	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28660581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28662800	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28663692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28667521	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28670261	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28675378	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28676909	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28681225	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28690018	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28701136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28705696	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707151	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]
rs28715777	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]
rs9888653	0.82[AFR][1000 genomes];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]
rs9920476	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920987	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv869747	chr15:72372245-72403103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	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
10	nsv510665	chr15:72374862-72407548	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv511557	chr15:72386175-72408069	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv569929	chr15:72386349-72403001	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72367200-72407600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:72372200-72399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:72375000-72408200	Weak transcription	Primary B cells from cord blood	blood
4	chr15:72379000-72407800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:72379800-72406200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:72380000-72407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:72389600-72403600	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:72390400-72407600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:72391200-72404200	Weak transcription	HSMMtube	muscle
10	chr15:72391800-72401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:72391800-72406600	Weak transcription	Ovary	ovary
12	chr15:72392600-72403000	Weak transcription	Fetal Intestine Small	intestine
13	chr15:72392600-72404000	Weak transcription	Fetal Stomach	stomach
14	chr15:72395200-72399400	Weak transcription	Fetal Heart	heart
15	chr15:72395800-72399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:72395800-72407800	Weak transcription	HMEC	breast
17	chr15:72395800-72409000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:72395800-72409200	Weak transcription	Gastric	stomach
19	chr15:72396000-72399000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:72396000-72399000	Weak transcription	Left Ventricle	heart
21	chr15:72396000-72399000	Weak transcription	Right Atrium	heart
22	chr15:72396000-72401400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:72396000-72401400	Weak transcription	Lung	lung
24	chr15:72396000-72402400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:72396000-72404200	Weak transcription	Osteobl	bone
26	chr15:72396000-72404600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:72396200-72404400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:72396400-72399400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:72396400-72408800	Weak transcription	Right Ventricle	heart
30	chr15:72396600-72399200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:72396600-72399200	Weak transcription	A549	lung
32	chr15:72396600-72400000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:72396600-72408200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:72396800-72399000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:72397000-72404200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:72397200-72404200	Weak transcription	Fetal Lung	lung
37	chr15:72397400-72404200	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:72397800-72399400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:72397800-72399400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:72397800-72408200	Weak transcription	Brain Angular Gyrus	brain
41	chr15:72397800-72408200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:72398600-72399800	Enhancers	Psoas Muscle	Psoas

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