Variant report

Variant	rs12593082
Chromosome Location	chr15:72461580-72461581
allele	G/T
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	EP300	chr15:72461252-72462101	T-47D	breast:	n/a	n/a
2	TCF12	chr15:72461575-72462143	ECC-1	luminal epithelium:	n/a	chr15:72461691-72461701
3	NFIC	chr15:72460733-72462249	ECC-1	luminal epithelium:	n/a	chr15:72461053-72461070
4	NFIC	chr15:72460802-72462203	ECC-1	luminal epithelium:	n/a	chr15:72461053-72461070
5	ESR1	chr15:72461559-72462274	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr15:72461485-72462332	ECC-1	luminal epithelium:	n/a	chr15:72461691-72461701

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72459821..72461687-chr15:72564383..72566445,2	MCF-7	breast:
2	chr15:72459257..72462704-chr15:72465780..72468461,3	MCF-7	breast:

Variant related genes	Relation type
GRAMD2	TF binding region
ENSG00000137817	Chromatin interaction
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11072341	0.88[ASN][1000 genomes]
rs11072343	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072344	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072355	1.00[CEU][hapmap]
rs1120002	0.88[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12439689	0.92[ASN][1000 genomes]
rs12440204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440299	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440435	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12440927	1.00[CEU][hapmap]
rs12441246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441470	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441567	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441622	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442680	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12443127	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592615	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592858	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592932	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592969	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593857	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12593946	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12594297	0.90[EUR][1000 genomes]
rs12911449	1.00[CEU][hapmap]
rs1426168	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1545825	0.84[ASN][1000 genomes]
rs16953770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16956539	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16956599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16956602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16956723	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1871834	0.81[ASN][1000 genomes]
rs2288256	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2305705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28397923	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28639924	0.88[ASN][1000 genomes]
rs28653163	0.88[ASN][1000 genomes]
rs28701834	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912226	1.00[CEU][hapmap]
rs2912229	1.00[CEU][hapmap]
rs2929521	0.84[ASN][1000 genomes]
rs2929522	0.84[ASN][1000 genomes]
rs2929530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2929533	0.81[ASN][1000 genomes]
rs2957369	0.84[ASN][1000 genomes]
rs2957741	0.84[ASN][1000 genomes]
rs2957747	0.84[ASN][1000 genomes]
rs2957749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2959915	1.00[CEU][hapmap]
rs34625473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35773391	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3803388	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3809505	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825869	0.84[ASN][1000 genomes]
rs4442765	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4511484	0.84[ASN][1000 genomes]
rs6495000	1.00[CEU][hapmap]
rs7161909	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7164646	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165735	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7171446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026894	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8029218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8039245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8192381	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9920148	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72448800-72462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:72449200-72462200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:72454400-72471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:72457800-72462000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:72458600-72463600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr15:72459600-72462600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:72459800-72461800	Enhancers	Fetal Heart	heart
8	chr15:72459800-72462400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:72459800-72463400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:72460000-72461800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:72460000-72461800	Enhancers	Fetal Brain Male	brain
12	chr15:72460000-72461800	Enhancers	Lung	lung
13	chr15:72460000-72463400	Enhancers	Fetal Intestine Large	intestine
14	chr15:72460400-72461600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:72460400-72461600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr15:72460400-72461600	Enhancers	Fetal Brain Female	brain
17	chr15:72460400-72461600	Enhancers	Fetal Muscle Leg	muscle
18	chr15:72460400-72461800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:72460400-72461800	Flanking Active TSS	HMEC	breast
20	chr15:72460400-72462000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr15:72460400-72462000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr15:72460400-72462000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:72460400-72462000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:72460400-72462000	Enhancers	Left Ventricle	heart
25	chr15:72460400-72462000	Enhancers	Dnd41	blood
26	chr15:72460400-72462200	Enhancers	Fetal Thymus	thymus
27	chr15:72460400-72462400	Enhancers	Primary hematopoietic stem cells	blood
28	chr15:72460600-72461600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:72460600-72461600	Enhancers	Brain Hippocampus Middle	brain
30	chr15:72460600-72461600	Flanking Active TSS	Fetal Lung	lung
31	chr15:72460600-72461800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:72460600-72461800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:72460600-72462200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:72460600-72462200	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:72460800-72461600	Enhancers	Right Ventricle	heart
36	chr15:72460800-72461800	Enhancers	Right Atrium	heart
37	chr15:72460800-72462600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:72460800-72462600	Flanking Active TSS	Placenta	Placenta
39	chr15:72461000-72461600	Enhancers	Brain Cingulate Gyrus	brain
40	chr15:72461000-72462800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr15:72461000-72463200	Enhancers	Stomach Mucosa	stomach
42	chr15:72461200-72462000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr15:72461200-72462400	Weak transcription	Gastric	stomach
44	chr15:72461200-72463600	Enhancers	Fetal Intestine Small	intestine
45	chr15:72461200-72464400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:72461400-72461600	Enhancers	Primary T cells from cord blood	blood
47	chr15:72461400-72462000	Bivalent Enhancer	Fetal Stomach	stomach
48	chr15:72461400-72462200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr15:72461400-72466800	Weak transcription	NHEK	skin

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