Variant report

Variant	rs28661594
Chromosome Location	chr15:72882457-72882458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72882454..72884361-chr15:72885367..72887543,2	MCF-7	breast:
2	chr15:72870050..72872612-chr15:72882296..72884014,2	MCF-7	breast:
3	chr15:72882042..72883837-chr15:72890523..72892478,2	MCF-7	breast:
4	chr15:72875994..72878313-chr15:72882141..72883878,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARIH1-1	chr15:72882032-72884186	ENSG00000260534.1

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10220917	1.00[ASN][1000 genomes]
rs11072372	1.00[ASN][1000 genomes]
rs12439127	1.00[ASN][1000 genomes]
rs13379855	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16953788	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956759	1.00[ASN][1000 genomes]
rs16956826	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16957154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957189	1.00[ASN][1000 genomes]
rs1816645	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1963894	1.00[ASN][1000 genomes]
rs28393893	1.00[ASN][1000 genomes]
rs28422889	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28435710	1.00[ASN][1000 genomes]
rs28437631	1.00[EUR][1000 genomes]
rs28439115	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28453701	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28471053	1.00[ASN][1000 genomes]
rs28488862	1.00[ASN][1000 genomes]
rs28493570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28534054	1.00[ASN][1000 genomes]
rs28541481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28795465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28832330	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28853391	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4777516	1.00[ASN][1000 genomes]
rs6495002	1.00[ASN][1000 genomes]
rs72735194	1.00[ASN][1000 genomes]
rs73440566	1.00[ASN][1000 genomes]
rs73440586	1.00[ASN][1000 genomes]
rs73442510	1.00[ASN][1000 genomes]
rs8039489	1.00[ASN][1000 genomes]
rs9806212	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806258	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806374	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9944261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534037	chr15:72659210-72964029	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	esv3430383	chr15:72821093-73035167	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72841000-72909000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:72870800-72887800	Weak transcription	Right Ventricle	heart
3	chr15:72870800-72896400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:72870800-72902200	Weak transcription	Gastric	stomach
5	chr15:72871600-72889400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:72873400-72883800	Weak transcription	Aorta	Aorta
7	chr15:72873600-72884400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:72874800-72899800	Weak transcription	Fetal Stomach	stomach
9	chr15:72876000-72883600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:72876200-72903400	Weak transcription	Brain Germinal Matrix	brain
11	chr15:72876200-72907800	Weak transcription	Brain Substantia Nigra	brain
12	chr15:72876400-72903800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:72876600-72883800	Weak transcription	HSMMtube	muscle
14	chr15:72876800-72882600	Weak transcription	Pancreas	Pancrea
15	chr15:72876800-72883000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:72876800-72883400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:72876800-72907600	Weak transcription	Lung	lung
18	chr15:72877200-72883200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:72877600-72883200	Weak transcription	Fetal Lung	lung
20	chr15:72877600-72889400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:72877800-72883200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:72877800-72910000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:72878000-72882600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:72878200-72884800	Weak transcription	Primary T cells from cord blood	blood
25	chr15:72878400-72882800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:72878400-72883200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:72878400-72883400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:72878400-72883400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:72878400-72883400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:72878400-72883600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:72878400-72883600	Weak transcription	Fetal Thymus	thymus
32	chr15:72878400-72883600	Weak transcription	Thymus	Thymus
33	chr15:72878400-72884000	Weak transcription	HMEC	breast
34	chr15:72878400-72884400	Weak transcription	Fetal Kidney	kidney
35	chr15:72878400-72907800	Weak transcription	Left Ventricle	heart
36	chr15:72878600-72883000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:72878600-72883000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:72878600-72883400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:72878800-72882800	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:72878800-72883200	Weak transcription	Placenta	Placenta
41	chr15:72878800-72883400	Weak transcription	A549	lung
42	chr15:72878800-72884400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:72879200-72882600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:72879400-72884000	Weak transcription	GM12878-XiMat	blood
45	chr15:72879800-72882600	Weak transcription	Osteobl	bone
46	chr15:72879800-72882800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:72879800-72883000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:72879800-72883600	Weak transcription	NH-A	brain
49	chr15:72879800-72906400	Weak transcription	Adipose Nuclei	Adipose
50	chr15:72880000-72892200	Weak transcription	Liver	Liver

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