Variant report

Variant	rs12441140
Chromosome Location	chr15:32975717-32975718
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	FOS	chr15:32975515-32975760	MCF10A-Er-Src	breast:	n/a	chr15:32975599-32975609 chr15:32975600-32975608 chr15:32975599-32975608 chr15:32975600-32975607 chr15:32975737-32975749
2	FOS	chr15:32974697-32975751	MCF10A-Er-Src	breast:	n/a	chr15:32975599-32975609 chr15:32975600-32975608 chr15:32975599-32975608 chr15:32975600-32975607 chr15:32975737-32975749
3	FOSL2	chr15:32974683-32975795	SK-N-SH	brain:	n/a	chr15:32975599-32975609 chr15:32975600-32975608 chr15:32975599-32975608 chr15:32975600-32975607 chr15:32975737-32975749
4	PBX3	chr15:32974581-32975978	SK-N-SH	brain:	n/a	chr15:32975732-32975741
5	FOS	chr15:32974666-32975849	MCF10A-Er-Src	breast:	n/a	chr15:32975599-32975609 chr15:32975600-32975608 chr15:32975599-32975608 chr15:32975600-32975607 chr15:32975737-32975749
6	MYC	chr15:32975427-32976718	MCF10A-Er-Src	breast:	n/a	chr15:32975599-32975608 chr15:32975600-32975609 chr15:32976471-32976481
7	STAT3	chr15:32975386-32976031	GM12878	blood:	n/a	chr15:32975599-32975608 chr15:32975600-32975609
8	MAFK	chr15:32975469-32977097	IMR90	lung:	n/a	n/a
9	POLR2A	chr15:32974499-32978248	IMR90	lung:	n/a	n/a
10	STAT3	chr15:32974733-32975751	MCF10A-Er-Src	breast:	n/a	chr15:32974889-32974900 chr15:32975599-32975608 chr15:32975600-32975609 chr15:32974969-32974977
11	FOS	chr15:32974727-32977396	MCF10A-Er-Src	breast:	n/a	chr15:32975599-32975609 chr15:32976583-32976594 chr15:32975600-32975608 chr15:32975599-32975608 chr15:32975600-32975607 chr15:32975737-32975749 chr15:32976103-32976114

Variant related genes	Relation type
SCG5	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12102176	0.98[ASN][1000 genomes]
rs12438604	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.99[ASN][1000 genomes]
rs12441136	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12442397	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28688414	0.94[ASN][1000 genomes]
rs35703183	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3817592	0.88[CEU][hapmap];0.83[CHB][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6494576	0.81[AMR][1000 genomes]
rs7170561	0.87[MEX][hapmap]
rs7177843	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.99[ASN][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	nsv431374	chr15:32008985-32976055	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469587	chr15:32821940-32986579	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv482780	chr15:32821940-32986579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv568915	chr15:32965357-32994056	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv456787	chr15:32968923-33023951	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv568916	chr15:32968923-33023951	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:32961200-32976200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:32961200-32980200	Weak transcription	Thymus	Thymus
3	chr15:32964600-32990800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:32964800-32993800	Weak transcription	Fetal Brain Male	brain
5	chr15:32965000-32983600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:32970000-32977800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:32970000-32982600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:32970200-32976200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:32970200-32977800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:32970200-32979400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:32970200-32979600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:32972000-32979400	Weak transcription	HepG2	liver
13	chr15:32972800-32976600	Strong transcription	Fetal Brain Female	brain
14	chr15:32973200-32986000	Weak transcription	Brain Germinal Matrix	brain
15	chr15:32973800-32976600	Enhancers	HSMM	muscle
16	chr15:32974000-32976200	Enhancers	NHEK	skin
17	chr15:32974000-32976800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:32974000-32977200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:32974000-32978400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:32974000-32981000	Enhancers	HMEC	breast
21	chr15:32974200-32976200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:32974200-32976600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:32974200-32977200	Enhancers	A549	lung
24	chr15:32974200-32977200	Enhancers	NHLF	lung
25	chr15:32974200-32978000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:32974400-32976600	Enhancers	Stomach Smooth Muscle	stomach
27	chr15:32974600-32976600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr15:32974600-32977000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr15:32974600-32977600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:32974800-32976000	Enhancers	Osteobl	bone
31	chr15:32974800-32977000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:32974800-32978400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:32974800-32978600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:32975000-32976600	Enhancers	HSMMtube	muscle
35	chr15:32975000-32977600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:32975000-32978600	Strong transcription	Liver	Liver
37	chr15:32975000-32983200	Weak transcription	Brain Substantia Nigra	brain
38	chr15:32975000-32983400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:32975200-32976000	Enhancers	NHDF-Ad	bronchial
40	chr15:32975200-32976400	Weak transcription	Aorta	Aorta
41	chr15:32975200-32976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:32975200-32977600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:32975200-32977800	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:32975200-32980200	Weak transcription	Placenta	Placenta
45	chr15:32975200-32983400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:32975200-32983800	Weak transcription	Brain Anterior Caudate	brain
47	chr15:32975200-32986000	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:32975400-32975800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:32975400-32975800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr15:32975400-32976400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links