Variant report

Variant	rs2267552
Chromosome Location	chr12:4793464-4793465
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	CTCF	chr12:4793420-4793570	GM06990	blood:	n/a	n/a

Variant related genes	Relation type
NDUFA9	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10082907	0.87[ASN][1000 genomes]
rs10083146	0.88[ASN][1000 genomes]
rs10083152	0.88[ASN][1000 genomes]
rs1009633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160902	0.82[ASN][1000 genomes]
rs1024655	0.90[ASN][1000 genomes]
rs10774256	0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs10774259	0.87[ASN][1000 genomes]
rs10774260	0.88[ASN][1000 genomes]
rs10849125	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10849127	0.86[CHB][hapmap]
rs10849130	0.81[CHB][hapmap]
rs10849131	0.86[CHB][hapmap]
rs10849133	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10849138	0.81[CHB][hapmap]
rs10849139	0.86[CHB][hapmap]
rs11063314	0.86[CHB][hapmap]
rs12296205	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1468556	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs17783373	0.82[ASN][1000 genomes]
rs1990310	0.88[ASN][1000 genomes]
rs2074984	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2109099	0.82[ASN][1000 genomes]
rs2109100	0.83[ASN][1000 genomes]
rs2159354	0.82[ASN][1000 genomes]
rs2159355	0.82[ASN][1000 genomes]
rs2191157	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2240761	0.99[ASN][1000 genomes]
rs2240762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286578	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2286580	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2302244	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359252	0.82[EUR][1000 genomes]
rs2359466	0.86[CHB][hapmap]
rs2359467	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs35049745	0.82[ASN][1000 genomes]
rs3782740	0.81[CHB][hapmap]
rs3782741	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3782742	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4147689	0.95[ASN][1000 genomes]
rs4147696	0.88[ASN][1000 genomes]
rs4765779	0.82[ASN][1000 genomes]
rs4765781	0.84[ASN][1000 genomes]
rs4765782	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4766272	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs4766276	0.82[ASN][1000 genomes]
rs4766278	0.82[ASN][1000 genomes]
rs4766279	0.82[ASN][1000 genomes]
rs4766280	0.82[ASN][1000 genomes]
rs4766281	0.82[ASN][1000 genomes]
rs4766282	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4766283	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4766286	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6489558	0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6489560	0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7132030	0.86[CHB][hapmap]
rs7136382	0.84[ASN][1000 genomes]
rs7136583	0.88[ASN][1000 genomes]
rs7137040	0.82[ASN][1000 genomes]
rs7137660	0.82[ASN][1000 genomes]
rs7305525	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs7306235	0.82[ASN][1000 genomes]
rs7311475	0.82[ASN][1000 genomes]
rs7311675	0.84[CHB][hapmap]
rs7311694	0.85[CHB][hapmap]
rs7312119	0.82[ASN][1000 genomes]
rs7312558	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7315211	0.86[CHB][hapmap]
rs7316209	0.86[CHB][hapmap]
rs7953170	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7953399	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs7966628	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7972019	0.82[ASN][1000 genomes]
rs7972501	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7975978	0.86[CHB][hapmap]
rs9300304	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer 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 target site	18 gene(s)	inside rSNPs	diseases
2	nsv1036308	chr12:4748657-4804156	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2267552	NDUFA9	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4759000-4799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:4773800-4794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:4778800-4794400	Weak transcription	Small Intestine	intestine
4	chr12:4778800-4796000	Weak transcription	NHEK	skin
5	chr12:4779000-4799000	Weak transcription	Stomach Mucosa	stomach
6	chr12:4779600-4801800	Weak transcription	K562	blood
7	chr12:4780200-4809200	Weak transcription	Fetal Heart	heart
8	chr12:4780600-4799000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:4781200-4794800	Weak transcription	NH-A	brain
10	chr12:4781400-4794600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:4782000-4796800	Weak transcription	Fetal Kidney	kidney
12	chr12:4782200-4794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:4782200-4796200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:4782200-4803200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:4782400-4796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:4787800-4810800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:4788600-4804400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr12:4788800-4800800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:4789000-4798200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:4789200-4799600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:4789600-4799400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:4789600-4800200	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:4789600-4800600	Strong transcription	Fetal Brain Female	brain
24	chr12:4790600-4798000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:4791000-4795600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:4791000-4796200	Strong transcription	HMEC	breast
27	chr12:4791000-4797400	Strong transcription	GM12878-XiMat	blood
28	chr12:4791000-4798000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:4791000-4798000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:4791000-4798200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:4791000-4798200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:4791000-4798200	Strong transcription	Placenta	Placenta
33	chr12:4791000-4798400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:4791000-4798400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:4791000-4798400	Strong transcription	Adipose Nuclei	Adipose
36	chr12:4791000-4798400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:4791000-4798600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:4791000-4799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:4791000-4799600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:4791000-4799600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:4791000-4799600	Strong transcription	Dnd41	blood
42	chr12:4791200-4795400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:4791200-4797600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:4791200-4797600	Strong transcription	HepG2	liver
45	chr12:4791200-4797800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:4791200-4797800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr12:4791200-4797800	Strong transcription	Rectal Smooth Muscle	rectum
48	chr12:4791200-4798000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:4791200-4798000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:4791200-4798000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links