Variant report

Variant	rs28718544
Chromosome Location	chr15:33398409-33398410
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	chr15:33359731..33361492-chr15:33397821..33400228,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-632K20.1.1-6	chr15:33397959-33398437	NONHSAT041540

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1026752	0.96[ASN][1000 genomes]
rs10519781	0.83[ASN][1000 genomes]
rs10519788	0.96[ASN][1000 genomes]
rs10775202	0.83[ASN][1000 genomes]
rs10851823	0.83[ASN][1000 genomes]
rs11072170	0.83[ASN][1000 genomes]
rs11072175	0.83[ASN][1000 genomes]
rs11072187	0.86[ASN][1000 genomes]
rs11636433	0.83[ASN][1000 genomes]
rs11639303	0.83[ASN][1000 genomes]
rs12439012	0.83[ASN][1000 genomes]
rs12440002	0.83[ASN][1000 genomes]
rs17235533	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17235547	0.83[ASN][1000 genomes]
rs2291064	0.96[ASN][1000 genomes]
rs2291065	0.96[ASN][1000 genomes]
rs2291066	0.92[ASN][1000 genomes]
rs2306278	0.83[ASN][1000 genomes]
rs28510826	0.96[ASN][1000 genomes]
rs28551066	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28576977	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345794	0.90[ASN][1000 genomes]
rs4779604	0.83[ASN][1000 genomes]
rs4779605	0.83[ASN][1000 genomes]
rs4779606	0.83[ASN][1000 genomes]
rs4780074	0.83[ASN][1000 genomes]
rs8033302	0.94[ASN][1000 genomes]
rs8039005	0.96[ASN][1000 genomes]
rs922510	0.83[ASN][1000 genomes]
rs922511	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28718544	FMN1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33397000-33401200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:33397000-33402400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:33397000-33403000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:33397200-33400200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:33397200-33403600	Weak transcription	Fetal Kidney	kidney
6	chr15:33397400-33400000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:33397600-33399600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:33397600-33399800	Weak transcription	Hela-S3	cervix
9	chr15:33397600-33406000	Weak transcription	NHEK	skin
10	chr15:33397800-33398800	Weak transcription	Osteobl	bone
11	chr15:33397800-33399000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:33397800-33399400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:33397800-33399600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:33397800-33399600	Weak transcription	HSMM	muscle
15	chr15:33397800-33403400	Weak transcription	HSMMtube	muscle
16	chr15:33398200-33399000	Weak transcription	NHDF-Ad	bronchial
17	chr15:33398200-33399600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:33398200-33399600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:33398200-33399600	Weak transcription	NHLF	lung
20	chr15:33398200-33400800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:33398400-33399600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:33398400-33400200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:33398400-33403200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:33398400-33406200	Weak transcription	Fetal Thymus	thymus

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