Variant report

Variant	rs2293445
Chromosome Location	chr12:49398862-49398863
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	GABPA	chr12:49398187-49398993	HL-60	blood:	n/a	chr12:49398711-49398718
2	SPI1	chr12:49398535-49398892	HL-60	blood:	n/a	chr12:49398656-49398669 chr12:49398708-49398721
3	SPI1	chr12:49398285-49398918	HL-60	blood:	n/a	chr12:49398656-49398669 chr12:49398708-49398721

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49390603..49394865-chr12:49395546..49401151,4	MCF-7	breast:
2	chr12:49391088..49392701-chr12:49397999..49400022,2	MCF-7	breast:

Variant related genes	Relation type
PRKAG1	TF binding region
ENSG00000181418	Chromatin interaction
ENSG00000257913	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10459221	0.81[ASN][1000 genomes]
rs10459232	0.81[ASN][1000 genomes]
rs1054442	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[ASN][1000 genomes]
rs10747559	0.86[ASN][1000 genomes]
rs10783299	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783300	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783301	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875906	0.94[ASN][1000 genomes]
rs10875908	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875910	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875911	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875912	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.97[ASN][1000 genomes]
rs10875913	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875914	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875915	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875917	0.81[ASN][1000 genomes]
rs10875918	0.80[ASN][1000 genomes]
rs11168822	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168827	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168838	0.83[ASN][1000 genomes]
rs11168839	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168850	0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1138908	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614738	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs12580349	0.84[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.86[ASN][1000 genomes]
rs12821008	0.80[ASN][1000 genomes]
rs2117029	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241726	0.88[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293446	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304275	0.84[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs34436857	0.90[ASN][1000 genomes]
rs3741619	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs3741622	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3782357	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580698	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs6580699	0.84[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs7296288	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs7300136	0.80[ASN][1000 genomes]
rs7969091	0.84[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs876333	0.96[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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2293445	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs2293445	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs2293445	DDN	cis	Muscle Skeletal	GTEx
rs2293445	RHEBL1	cis	parietal	SCAN
rs2293445	RHEBL1	cis	cerebellum	SCAN
rs2293445	NCKAP5L	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49394000-49399400	Strong transcription	NHEK	skin
2	chr12:49394000-49400400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:49394200-49399600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:49394200-49399800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:49394200-49399800	Strong transcription	Placenta	Placenta
6	chr12:49394200-49400400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:49394400-49399600	Strong transcription	Adipose Nuclei	Adipose
8	chr12:49394400-49399600	Strong transcription	Fetal Intestine Small	intestine
9	chr12:49394400-49399600	Strong transcription	K562	blood
10	chr12:49394400-49399600	Strong transcription	NHLF	lung
11	chr12:49394400-49399800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:49394400-49399800	Strong transcription	Dnd41	blood
13	chr12:49394400-49400400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:49394400-49400400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:49394600-49399600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:49394600-49399600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr12:49394600-49399800	Strong transcription	Liver	Liver
18	chr12:49394600-49399800	Strong transcription	Fetal Thymus	thymus
19	chr12:49394600-49399800	ZNF genes & repeats	Ovary	ovary
20	chr12:49394600-49400400	Strong transcription	NH-A	brain
21	chr12:49394600-49401400	Strong transcription	Osteobl	bone
22	chr12:49394800-49399200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:49394800-49399600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr12:49394800-49399600	Strong transcription	Colonic Mucosa	Colon
25	chr12:49394800-49399600	Strong transcription	Esophagus	oesophagus
26	chr12:49394800-49399600	Strong transcription	HMEC	breast
27	chr12:49394800-49399800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:49394800-49400000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:49394800-49400200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:49394800-49400200	Strong transcription	Left Ventricle	heart
31	chr12:49394800-49400400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:49394800-49400400	Strong transcription	Brain Hippocampus Middle	brain
33	chr12:49394800-49403200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:49394800-49405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:49395000-49399400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:49395000-49399400	Strong transcription	Right Ventricle	heart
37	chr12:49395000-49399600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:49395000-49399600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:49395000-49399800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:49395000-49399800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:49395000-49399800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:49395000-49399800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:49395000-49399800	Strong transcription	Brain Anterior Caudate	brain
44	chr12:49395000-49399800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:49395000-49400000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:49395000-49400000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:49395000-49400000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:49395000-49400200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:49395000-49400200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:49395000-49401400	Strong transcription	GM12878-XiMat	blood

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