Variant report

Variant	rs13316462
Chromosome Location	chr3:112995529-112995530
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	POLR2A	chr3:112995020-112995536	GM12892	blood:	n/a	n/a
2	SPI1	chr3:112994994-112995650	GM12891	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
3	SPI1	chr3:112994871-112995720	GM12878	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
4	SPI1	chr3:112995077-112995623	GM12878	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
5	SPI1	chr3:112995071-112995702	GM12891	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
6	SPI1	chr3:112995186-112995577	HL-60	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
7	MTA3	chr3:112994867-112995765	GM12878	blood:	n/a	n/a
8	IRF1	chr3:112995318-112995594	K562	blood:	n/a	chr3:112995417-112995437 chr3:112995421-112995435 chr3:112995425-112995436 chr3:112995423-112995436 chr3:112995424-112995438 chr3:112995525-112995539 chr3:112995527-112995541 chr3:112995423-112995436 chr3:112995527-112995534 chr3:112995422-112995436
9	EP300	chr3:112994544-112995574	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr3:112994789-112995559	U87	brain:	n/a	n/a
11	POLR2A	chr3:112994768-112995616	U87	brain:	n/a	n/a
12	TCF12	chr3:112994586-112995538	ECC-1	luminal epithelium:	n/a	chr3:112994836-112994846 chr3:112995129-112995137

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112994340..112996390-chr3:112999455..113002856,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11717082	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11916824	1.00[EUR][1000 genomes]
rs13315100	1.00[EUR][1000 genomes]
rs1381062	1.00[EUR][1000 genomes]
rs1486896	1.00[EUR][1000 genomes]
rs1563932	1.00[EUR][1000 genomes]
rs16860752	1.00[ASW][hapmap]
rs16860782	1.00[ASW][hapmap]
rs16861019	1.00[ASW][hapmap]
rs1797613	1.00[EUR][1000 genomes]
rs1797618	1.00[EUR][1000 genomes]
rs2045689	1.00[EUR][1000 genomes]
rs2613918	1.00[EUR][1000 genomes]
rs2613924	1.00[EUR][1000 genomes]
rs2613930	1.00[EUR][1000 genomes]
rs2613953	1.00[EUR][1000 genomes]
rs2613955	1.00[EUR][1000 genomes]
rs2613965	1.00[EUR][1000 genomes]
rs2613966	1.00[EUR][1000 genomes]
rs2613969	1.00[EUR][1000 genomes]
rs2650095	1.00[EUR][1000 genomes]
rs2700195	1.00[EUR][1000 genomes]
rs2700196	1.00[TSI][hapmap]
rs2700197	1.00[EUR][1000 genomes]
rs2700211	1.00[EUR][1000 genomes]
rs2700213	1.00[EUR][1000 genomes]
rs2700228	1.00[EUR][1000 genomes]
rs2926810	1.00[EUR][1000 genomes]
rs2951457	1.00[EUR][1000 genomes]
rs3856722	1.00[EUR][1000 genomes]
rs4082653	1.00[ASW][hapmap]
rs4682135	1.00[EUR][1000 genomes]
rs57228683	1.00[EUR][1000 genomes]
rs57766030	1.00[EUR][1000 genomes]
rs57995695	1.00[EUR][1000 genomes]
rs58100446	1.00[EUR][1000 genomes]
rs59069330	1.00[EUR][1000 genomes]
rs59171219	1.00[EUR][1000 genomes]
rs59534035	1.00[EUR][1000 genomes]
rs59923952	1.00[EUR][1000 genomes]
rs6438141	1.00[EUR][1000 genomes]
rs6795832	1.00[TSI][hapmap]
rs6798990	1.00[EUR][1000 genomes]
rs712528	1.00[EUR][1000 genomes]
rs7615891	1.00[EUR][1000 genomes]
rs7623507	1.00[EUR][1000 genomes]
rs7629976	1.00[EUR][1000 genomes]
rs799828	1.00[EUR][1000 genomes]
rs9826018	1.00[EUR][1000 genomes]
rs9864636	1.00[EUR][1000 genomes]
rs9873004	1.00[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
2	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
5	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
7	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:112990600-113004000	Weak transcription	NHEK	skin
10	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:112993000-112995600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:112993000-112996200	Enhancers	Fetal Thymus	thymus
13	chr3:112993000-112997000	Weak transcription	Fetal Intestine Small	intestine
14	chr3:112993400-112995800	Enhancers	Fetal Brain Male	brain
15	chr3:112993400-112996200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:112993400-112996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
18	chr3:112993600-112995600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:112993600-112995800	Enhancers	Fetal Kidney	kidney
20	chr3:112993600-112996200	Genic enhancers	Fetal Lung	lung
21	chr3:112993800-112996400	Enhancers	Brain Angular Gyrus	brain
22	chr3:112993800-112997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
24	chr3:112994000-112995800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:112994000-112995800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:112994200-112995600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:112994200-112997800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:112994400-112995600	Flanking Active TSS	HepG2	liver
29	chr3:112994400-112996400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:112994600-112995800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:112994600-112995800	Flanking Active TSS	NHDF-Ad	bronchial
32	chr3:112994600-112996200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr3:112994800-112995600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:112994800-112995600	Weak transcription	Spleen	Spleen
35	chr3:112994800-112995800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:112994800-112995800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr3:112994800-112995800	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr3:112994800-112995800	Flanking Active TSS	NH-A	brain
39	chr3:112994800-112996000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:112994800-112996200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr3:112994800-112997400	Weak transcription	Gastric	stomach
42	chr3:112995000-112995600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:112995000-112995600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr3:112995000-112995600	Flanking Active TSS	HMEC	breast
45	chr3:112995000-112995600	Enhancers	K562	blood
46	chr3:112995000-112995800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:112995000-112995800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr3:112995000-112995800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:112995000-112995800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr3:112995000-112995800	Flanking Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links