Variant report

Variant	rs58415206
Chromosome Location	chr15:45569955-45569956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45454944..45455772-chr15:45568916..45570015,4	MCF-7	breast:
2	chr15:45464381..45467214-chr15:45569783..45571800,2	MCF-7	breast:
3	chr12:70683116..70683960-chr15:45569736..45570428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138606	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10519020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1618422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16941188	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16941213	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs16941242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1706766	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1706769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1706771	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1706773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1719233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2458226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57259026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61449949	0.91[AMR][1000 genomes]
rs6493142	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74009617	0.81[AMR][1000 genomes]
rs8033317	0.90[AFR][1000 genomes];0.84[AMR][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer 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	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	esv2282019	chr15:45569842-45570398	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3408029	chr15:45569939-45570344	Weak transcription Enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3513810	chr15:45569953-45570279	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45550200-45570600	Weak transcription	Stomach Mucosa	stomach
2	chr15:45552600-45570600	Weak transcription	Pancreas	Pancrea
3	chr15:45558000-45570400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:45560600-45570400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:45560600-45570600	Weak transcription	Fetal Stomach	stomach
6	chr15:45563000-45570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:45564800-45570400	Weak transcription	Fetal Brain Female	brain
8	chr15:45566000-45570400	Weak transcription	Brain Anterior Caudate	brain
9	chr15:45567200-45570400	Weak transcription	A549	lung
10	chr15:45567800-45570400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:45568800-45570400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:45568800-45570400	Enhancers	HepG2	liver
13	chr15:45569000-45570400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr15:45569000-45570400	Enhancers	Fetal Intestine Small	intestine
15	chr15:45569000-45570600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:45569000-45570600	Enhancers	Brain Angular Gyrus	brain
17	chr15:45569200-45570200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:45569200-45570200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:45569200-45570200	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:45569200-45570200	Weak transcription	Fetal Intestine Large	intestine
21	chr15:45569200-45570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:45569200-45570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:45569200-45570400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:45569200-45570400	Weak transcription	Brain Germinal Matrix	brain
25	chr15:45569400-45570200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:45569400-45570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:45569400-45570400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:45569400-45570400	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:45569400-45570400	Weak transcription	Brain Substantia Nigra	brain
30	chr15:45569600-45570000	Enhancers	Fetal Kidney	kidney
31	chr15:45569600-45570400	Enhancers	HMEC	breast
32	chr15:45569800-45570200	Weak transcription	Liver	Liver

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