Variant report

Variant	rs58299587
Chromosome Location	chr15:78502395-78502396
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:78501509-78502753	MCF-7	breast:	n/a	chr15:78502120-78502133
2	TCF12	chr15:78501412-78502841	ECC-1	luminal epithelium:	n/a	n/a
3	GATA3	chr15:78501599-78502785	MCF-7	breast:	n/a	chr15:78502120-78502133
4	POLR2A	chr15:78502282-78502625	ECC-1	luminal epithelium:	n/a	n/a
5	TCF7L2	chr15:78502216-78502705	MCF-7	breast:	n/a	n/a
6	GATA3	chr15:78501778-78502565	MCF-7	breast:	n/a	chr15:78502120-78502133
7	CEBPB	chr15:78502372-78502732	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr15:78502327-78502552	Hela-S3	cervix:	n/a	n/a
9	NFIC	chr15:78501581-78502895	ECC-1	luminal epithelium:	n/a	n/a
10	ZNF217	chr15:78501701-78502797	MCF-7	breast:	n/a	n/a
11	TCF7L2	chr15:78502301-78502669	Hela-S3	cervix:	n/a	n/a
12	MAX	chr15:78502247-78502805	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr15:78501479-78502896	ECC-1	luminal epithelium:	n/a	chr15:78502788-78502797 chr15:78501503-78501516
14	CTCF	chr15:78502340-78502490	HEK293	kidney:	n/a	chr15:78502429-78502442
15	NFIC	chr15:78501517-78502954	ECC-1	luminal epithelium:	n/a	n/a
16	TCF12	chr15:78501466-78502947	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78440397..78443186-chr15:78499689..78503898,3	MCF-7	breast:
2	chr15:78433373..78437251-chr15:78499302..78502813,3	MCF-7	breast:
3	chr15:78496538..78499859-chr15:78500154..78502705,3	MCF-7	breast:
4	chr15:78496325..78498387-chr15:78501053..78503232,2	MCF-7	breast:

Variant related genes	Relation type
ACSBG1	TF binding region
ENSG00000166411	Chromatin interaction
ENSG00000260988	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1011173	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12441219	0.82[EUR][1000 genomes]
rs28452388	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28722516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57021464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57491843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59398201	0.82[ASN][1000 genomes]
rs60968764	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62009347	0.82[ASN][1000 genomes]
rs62009348	0.82[ASN][1000 genomes]
rs62009353	0.82[ASN][1000 genomes]
rs62011375	0.82[ASN][1000 genomes]
rs62011377	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78493800-78504200	Enhancers	Brain Substantia Nigra	brain
2	chr15:78494200-78508800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr15:78494200-78509800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr15:78494800-78508800	Enhancers	Brain Hippocampus Middle	brain
5	chr15:78494800-78509800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr15:78495000-78504200	Enhancers	Brain Cingulate Gyrus	brain
7	chr15:78495400-78502600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:78495400-78510000	Enhancers	Pancreas	Pancrea
9	chr15:78495400-78511000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr15:78496000-78507200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:78496400-78507800	Enhancers	Brain Anterior Caudate	brain
12	chr15:78497200-78503800	Weak transcription	Lung	lung
13	chr15:78497200-78506800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr15:78498400-78503400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:78499200-78504000	Weak transcription	Right Ventricle	heart
16	chr15:78499600-78504400	Weak transcription	NHDF-Ad	bronchial
17	chr15:78499600-78504600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:78499600-78504800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:78499800-78502400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:78499800-78502400	Weak transcription	Osteobl	bone
21	chr15:78499800-78503600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:78500000-78504400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:78500800-78502600	Enhancers	Fetal Muscle Trunk	muscle
24	chr15:78500800-78506200	Enhancers	Brain Angular Gyrus	brain
25	chr15:78501200-78502600	Enhancers	Placenta	Placenta
26	chr15:78501200-78503400	Enhancers	Fetal Muscle Leg	muscle
27	chr15:78501200-78506200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:78501400-78502600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:78501400-78502600	Enhancers	Esophagus	oesophagus
30	chr15:78501400-78502800	Enhancers	NHEK	skin
31	chr15:78501400-78503000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:78501400-78503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:78501400-78503400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr15:78501400-78506000	Enhancers	Stomach Mucosa	stomach
35	chr15:78501600-78506000	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:78501600-78506600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:78501800-78502600	Enhancers	Adipose Nuclei	Adipose
38	chr15:78501800-78502600	Enhancers	Colonic Mucosa	Colon
39	chr15:78501800-78502600	Enhancers	Gastric	stomach
40	chr15:78501800-78502600	Enhancers	Left Ventricle	heart
41	chr15:78501800-78503000	Enhancers	Rectal Smooth Muscle	rectum
42	chr15:78501800-78503000	Enhancers	HSMMtube	muscle
43	chr15:78501800-78503200	Enhancers	Psoas Muscle	Psoas
44	chr15:78501800-78505800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr15:78502000-78502400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:78502000-78502600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr15:78502000-78503000	Flanking Active TSS	Hela-S3	cervix
48	chr15:78502000-78503400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:78502000-78503400	Enhancers	Stomach Smooth Muscle	stomach
50	chr15:78502000-78504200	Weak transcription	Right Atrium	heart

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