Variant report

Variant	rs12439137
Chromosome Location	chr15:51516304-51516305
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	CEBPB	chr15:51516025-51516406	Hela-S3	cervix:	n/a	chr15:51516264-51516275
2	MAFK	chr15:51515951-51516430	IMR90	lung:	n/a	chr15:51516045-51516055 chr15:51516272-51516287
3	CEBPB	chr15:51516111-51516453	IMR90	lung:	n/a	chr15:51516264-51516275
4	MAX	chr15:51515904-51516423	NB4	blood:	n/a	n/a
5	FOS	chr15:51515836-51517036	HUVEC	blood vessel:	n/a	chr15:51516045-51516053 chr15:51516045-51516052 chr15:51516043-51516054
6	MAFK	chr15:51516131-51516434	HepG2	liver:	n/a	chr15:51516272-51516287
7	MAFF	chr15:51516135-51516349	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:51516260-51516410	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr15:51515794-51516450	U87	brain:	n/a	n/a
10	MYC	chr15:51515971-51516496	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr15:51515876-51516506	MCF10A-Er-Src	breast:	n/a	chr15:51516314-51516325
12	POLR2A	chr15:51515794-51516424	U87	brain:	n/a	n/a
13	FOS	chr15:51515850-51516494	MCF10A-Er-Src	breast:	n/a	chr15:51516045-51516053 chr15:51516045-51516052 chr15:51516043-51516054
14	STAT3	chr15:51515875-51516524	MCF10A-Er-Src	breast:	n/a	chr15:51516314-51516325
15	STAT3	chr15:51515876-51516763	MCF10A-Er-Src	breast:	n/a	chr15:51516314-51516325
16	FOS	chr15:51515908-51516522	MCF10A-Er-Src	breast:	n/a	chr15:51516045-51516053 chr15:51516045-51516052 chr15:51516043-51516054
17	E2F4	chr15:51515974-51516443	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr15:51515972-51516460	MCF10A-Er-Src	breast:	n/a	chr15:51516314-51516325
19	STAT3	chr15:51515829-51516539	MCF10A-Er-Src	breast:	n/a	chr15:51516314-51516325
20	MAFK	chr15:51516195-51516392	HepG2	liver:	n/a	chr15:51516272-51516287
21	MYC	chr15:51515725-51516505	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr15:51515857-51516518	MCF10A-Er-Src	breast:	n/a	chr15:51516045-51516053 chr15:51516045-51516052 chr15:51516043-51516054
23	MAFF	chr15:51516133-51516366	K562	blood:	n/a	n/a
24	GATA3	chr15:51515968-51516431	T-47D	breast:	n/a	n/a
25	SP1	chr15:51515674-51516339	HCT-116	colon:	n/a	n/a
26	FOS	chr15:51515724-51516462	MCF10A-Er-Src	breast:	n/a	chr15:51516045-51516053 chr15:51516045-51516052 chr15:51516043-51516054

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51514557..51518713-chr15:51518929..51521836,3	K562	blood:
2	chr15:51515145..51517510-chr15:51519278..51520848,2	MCF-7	breast:

Variant related genes	Relation type
CYP19A1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12148492	1.00[JPT][hapmap]
rs12441170	1.00[JPT][hapmap]
rs12442028	1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs12443032	1.00[JPT][hapmap]
rs16964215	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes]
rs17524318	1.00[JPT][hapmap]
rs17601241	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes]
rs17602588	1.00[JPT][hapmap]
rs2414099	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28694260	0.83[AMR][1000 genomes]
rs28757168	0.91[AMR][1000 genomes]
rs4774585	1.00[JPT][hapmap]
rs4774586	1.00[JPT][hapmap]
rs4774587	1.00[JPT][hapmap]
rs55736385	0.91[AMR][1000 genomes]
rs55845908	0.89[AMR][1000 genomes]
rs56114735	0.81[AMR][1000 genomes]
rs72727164	0.89[AMR][1000 genomes]
rs72727165	0.89[AMR][1000 genomes]
rs72727168	0.89[AMR][1000 genomes]
rs732762	1.00[JPT][hapmap]
rs8025191	1.00[JPT][hapmap]
rs8025374	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8041933	1.00[JPT][hapmap]
rs934633	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs9944225	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12439137	EMR1	trans	lymphoblastoid	seeQTL
rs12439137	SLC30A4	cis	cerebellum	SCAN
rs12439137	FGF7	cis	cerebellum	SCAN
rs12439137	TRPM7	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51500000-51520000	Strong transcription	Placenta	Placenta
2	chr15:51501400-51518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:51513200-51520400	Weak transcription	HepG2	liver
4	chr15:51515000-51516400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr15:51515200-51516400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:51515200-51517400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:51515200-51517600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:51515200-51519600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:51515200-51520400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:51515200-51521000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr15:51515200-51521600	Enhancers	NHDF-Ad	bronchial
12	chr15:51515400-51517200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:51515400-51517400	Enhancers	HSMM	muscle
14	chr15:51515400-51517400	Enhancers	Osteobl	bone
15	chr15:51515400-51520600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:51515600-51516400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:51515600-51516800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr15:51515600-51517400	Enhancers	HSMMtube	muscle
19	chr15:51515800-51516400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:51515800-51516400	Enhancers	Brain Substantia Nigra	brain
21	chr15:51515800-51516600	Enhancers	Adipose Nuclei	Adipose
22	chr15:51515800-51517000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:51515800-51517200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:51515800-51517200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:51515800-51517400	Enhancers	HUVEC	blood vessel
26	chr15:51515800-51517400	Enhancers	NHLF	lung
27	chr15:51515800-51517600	Enhancers	HMEC	breast
28	chr15:51516000-51516400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:51516000-51516400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:51516000-51516600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:51516000-51516600	Enhancers	Hela-S3	cervix
32	chr15:51516000-51517000	Weak transcription	Gastric	stomach
33	chr15:51516200-51516400	Enhancers	Aorta	Aorta
34	chr15:51516200-51516600	Flanking Active TSS	NH-A	brain
35	chr15:51516200-51516800	Enhancers	Brain Hippocampus Middle	brain
36	chr15:51516200-51520000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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