Variant report

Variant	rs8025960
Chromosome Location	chr15:79096673-79096674
allele	A/G
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	TEAD4	chr15:79096621-79097220	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr15:79096610-79097283	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr15:79096583-79097259	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr15:79096635-79097234	ECC-1	luminal epithelium:	n/a	n/a
5	NR3C1	chr15:79096655-79097098	ECC-1	luminal epithelium:	n/a	chr15:79096985-79096992 chr15:79096928-79096941 chr15:79096842-79096849
6	ESR1	chr15:79096622-79097199	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr15:79096555-79097303	ECC-1	luminal epithelium:	n/a	n/a
8	NFIC	chr15:79096599-79097302	ECC-1	luminal epithelium:	n/a	n/a
9	ESR1	chr15:79096592-79097143	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr15:79096570-79097360	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr15:79096620-79097221	ECC-1	luminal epithelium:	n/a	n/a
12	TCF12	chr15:79096575-79097297	ECC-1	luminal epithelium:	n/a	n/a
13	FOXM1	chr15:79096644-79097213	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79095528..79098098-chr15:79101910..79104531,2	MCF-7	breast:

Variant related genes	Relation type
ADAMTS7	TF binding region
ENSG00000136378	Chromatin interaction
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12437868	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12438008	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.85[ASN][1000 genomes]
rs12440925	0.91[ASN][1000 genomes]
rs2277547	0.82[CHB][hapmap];0.82[CHD][hapmap];0.87[ASN][1000 genomes]
rs28691842	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2869862	0.83[ASN][1000 genomes]
rs3743058	0.87[ASN][1000 genomes]
rs58676916	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61393924	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62014860	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495329	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6495330	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7169068	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7183257	0.88[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	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
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv977740	chr15:79094929-79099012	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79072000-79096800	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:79072800-79102400	Weak transcription	Fetal Kidney	kidney
3	chr15:79082800-79102200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:79083200-79102000	Weak transcription	Fetal Heart	heart
5	chr15:79083800-79102400	Weak transcription	Aorta	Aorta
6	chr15:79088200-79096800	Weak transcription	Brain Angular Gyrus	brain
7	chr15:79088800-79102600	Weak transcription	Ovary	ovary
8	chr15:79090200-79101000	Weak transcription	Fetal Lung	lung
9	chr15:79090200-79101000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:79090400-79096800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:79090600-79097000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:79090800-79096800	Weak transcription	Left Ventricle	heart
13	chr15:79090800-79101000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:79090800-79101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:79090800-79101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:79090800-79102200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:79091200-79098800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:79091200-79101400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:79091200-79101400	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:79091200-79101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:79091200-79101800	Weak transcription	Right Atrium	heart
22	chr15:79091200-79102200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:79091200-79102200	Weak transcription	Osteobl	bone
24	chr15:79091400-79101400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:79091400-79102000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:79093000-79096800	Weak transcription	Fetal Brain Female	brain
27	chr15:79093000-79102400	Weak transcription	Right Ventricle	heart
28	chr15:79093200-79102000	Weak transcription	Fetal Stomach	stomach
29	chr15:79094000-79099800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:79095000-79099200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr15:79095600-79098400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:79095800-79097200	Strong transcription	HSMMtube	muscle
33	chr15:79096000-79096800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr15:79096000-79096800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr15:79096000-79097600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:79096200-79096800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:79096200-79096800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:79096200-79096800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:79096200-79098800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr15:79096200-79099000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr15:79096200-79099000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:79096200-79099200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr15:79096400-79096800	Enhancers	Brain Anterior Caudate	brain
44	chr15:79096400-79096800	Enhancers	Brain Hippocampus Middle	brain
45	chr15:79096400-79097200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:79096400-79097200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr15:79096400-79097200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:79096400-79097600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr15:79096400-79097800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:79096400-79099000	Enhancers	HUES48 Cell Line	embryonic stem cell

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