Variant report

Variant	rs10774256
Chromosome Location	chr12:4780474-4780475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4758381..4761405-chr12:4778974..4782071,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10082907	0.86[ASN][1000 genomes]
rs10083146	0.85[ASN][1000 genomes]
rs10083152	0.87[ASN][1000 genomes]
rs1009633	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1024655	0.86[ASN][1000 genomes]
rs10774259	0.86[ASN][1000 genomes]
rs10774260	0.87[ASN][1000 genomes]
rs10849125	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10849127	0.81[CHB][hapmap]
rs10849131	0.81[CHB][hapmap]
rs10849133	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10849139	0.81[CHB][hapmap]
rs11063314	0.81[CHB][hapmap]
rs12296205	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1468556	0.82[CHD][hapmap]
rs1990310	0.85[ASN][1000 genomes]
rs2074984	0.81[JPT][hapmap]
rs2191157	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2240761	0.95[ASN][1000 genomes]
rs2240762	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2267552	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]
rs2286578	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2286580	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2302244	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2359466	0.81[CHB][hapmap]
rs2359467	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs3782741	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs3782742	0.81[CHB][hapmap]
rs4147689	0.99[ASN][1000 genomes]
rs4147696	0.85[ASN][1000 genomes]
rs4765781	0.80[ASN][1000 genomes]
rs4765782	0.95[JPT][hapmap]
rs4766272	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4766282	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4766283	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4766286	0.81[CHB][hapmap]
rs6489558	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6489560	0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7132030	0.81[CHB][hapmap]
rs7136382	0.80[ASN][1000 genomes]
rs7136583	0.84[ASN][1000 genomes]
rs7305525	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7311694	0.80[CHB][hapmap]
rs7315211	0.81[CHB][hapmap]
rs7316209	0.81[CHB][hapmap]
rs7953170	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7953399	0.81[CHB][hapmap]
rs7966628	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7972501	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7975978	0.81[CHB][hapmap]
rs9300304	0.81[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
rs10774256	NDUFA9	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr12:4760800-4782400	Strong transcription	Primary T cells from cord blood	blood
3	chr12:4761800-4782200	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:4762200-4783600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:4762600-4782800	Strong transcription	Adipose Nuclei	Adipose
6	chr12:4762800-4781000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:4762800-4782000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:4763000-4782200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:4763000-4782400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:4763000-4782400	Strong transcription	Placenta	Placenta
11	chr12:4763000-4783000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr12:4763200-4782200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:4763400-4781200	Strong transcription	GM12878-XiMat	blood
14	chr12:4763400-4781200	Strong transcription	NH-A	brain
15	chr12:4763400-4781400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:4763400-4781600	Strong transcription	Brain Anterior Caudate	brain
17	chr12:4763400-4781600	Strong transcription	Dnd41	blood
18	chr12:4763400-4782000	Strong transcription	Fetal Kidney	kidney
19	chr12:4763400-4782200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:4763400-4782200	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr12:4763400-4782200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:4763400-4782200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr12:4763400-4782400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:4763400-4782400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:4763400-4782400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:4763400-4782600	Strong transcription	Liver	Liver
27	chr12:4763400-4782600	Strong transcription	Fetal Intestine Large	intestine
28	chr12:4763400-4782800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:4763400-4782800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:4763400-4782800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:4763400-4783000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:4763400-4783000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:4763400-4783000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:4763400-4783000	Strong transcription	Fetal Lung	lung
35	chr12:4763400-4783000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:4763600-4780600	Strong transcription	Primary B cells from cord blood	blood
37	chr12:4763600-4782400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:4763600-4782400	Strong transcription	Left Ventricle	heart
39	chr12:4766400-4782400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:4766600-4782400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:4766800-4781200	Strong transcription	Brain Angular Gyrus	brain
42	chr12:4771200-4781000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:4772600-4782400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:4773000-4783000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:4773600-4782400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:4773800-4782800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:4773800-4794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:4774000-4781200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:4774000-4782200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:4774000-4782400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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