Variant report

Variant	rs61294562
Chromosome Location	chr15:39724400-39724401
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39721051..39725636-chr15:39870055..39875310,7	MCF-7	breast:
2	chr15:39464240..39465905-chr15:39723603..39725817,2	MCF-7	breast:
3	chr15:39724107..39725948-chr15:39841990..39843603,2	MCF-7	breast:
4	chr15:39723566..39727788-chr15:39872507..39874775,4	MCF-7	breast:
5	chr15:39721562..39724453-chr15:39734811..39737253,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs58001045	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58836677	1.00[AMR][1000 genomes]
rs59550930	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59611156	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59752089	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60077096	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60658485	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60729119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60772140	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60780722	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61052847	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61140941	1.00[AMR][1000 genomes]
rs61583976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393465	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393501	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395320	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395324	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395338	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395340	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397317	1.00[AMR][1000 genomes]
rs73397334	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397367	1.00[AMR][1000 genomes]
rs8028168	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39713200-39727400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:39719200-39728200	Enhancers	HUVEC	blood vessel
3	chr15:39719400-39726800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:39719600-39725000	Weak transcription	Right Ventricle	heart
5	chr15:39719600-39727200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:39719800-39725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:39720200-39725000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:39720200-39725000	Weak transcription	Fetal Stomach	stomach
9	chr15:39720200-39725600	Weak transcription	Lung	lung
10	chr15:39720200-39726800	Weak transcription	Adipose Nuclei	Adipose
11	chr15:39720400-39726400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr15:39721600-39724400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:39721600-39724600	Enhancers	Osteobl	bone
14	chr15:39721800-39724400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:39721800-39725400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:39722400-39727800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:39722600-39725000	Weak transcription	NHDF-Ad	bronchial
18	chr15:39722600-39725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:39722600-39725600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:39722600-39726800	Weak transcription	Small Intestine	intestine
21	chr15:39722600-39727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:39722800-39725600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:39722800-39725600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:39722800-39730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:39723000-39725000	Weak transcription	HepG2	liver
26	chr15:39723000-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:39723000-39726800	Weak transcription	Stomach Mucosa	stomach
28	chr15:39723000-39727000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:39723200-39724400	Weak transcription	NHEK	skin
30	chr15:39723200-39725200	Weak transcription	Left Ventricle	heart
31	chr15:39723200-39725200	Weak transcription	HMEC	breast
32	chr15:39723200-39725400	Weak transcription	Primary T cells from cord blood	blood
33	chr15:39723400-39725400	Weak transcription	Fetal Thymus	thymus
34	chr15:39723600-39725200	Weak transcription	Fetal Lung	lung
35	chr15:39723800-39724800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:39723800-39725400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:39723800-39725400	Enhancers	Stomach Smooth Muscle	stomach
38	chr15:39723800-39727400	Enhancers	Colon Smooth Muscle	Colon
39	chr15:39723800-39731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:39724000-39724600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:39724000-39725600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:39724000-39725600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:39724000-39727000	Weak transcription	NH-A	brain
44	chr15:39724000-39728000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:39724200-39724400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:39724200-39724400	Enhancers	Fetal Heart	heart
47	chr15:39724200-39724400	Enhancers	Right Atrium	heart
48	chr15:39724200-39724400	Enhancers	Spleen	Spleen
49	chr15:39724200-39724400	Enhancers	HSMMtube	muscle
50	chr15:39724200-39724600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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