Variant report

Variant	rs11189274
Chromosome Location	chr10:99311629-99311630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99307089..99309387-chr10:99309451..99312013,2	MCF-7	breast:
2	chr10:99203371..99205386-chr10:99311046..99312878,2	K562	blood:
3	chr10:99296840..99298523-chr10:99309435..99312063,2	MCF-7	breast:
4	chr10:99303622..99306407-chr10:99309864..99312001,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10748698	0.80[EUR][1000 genomes]
rs10748699	0.95[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs10748700	0.84[EUR][1000 genomes]
rs10882957	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882959	0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs10882961	0.84[EUR][1000 genomes]
rs10882962	0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs10882963	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882965	0.86[EUR][1000 genomes]
rs10882966	0.83[EUR][1000 genomes]
rs10882967	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1107517	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1107518	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189267	0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs11189270	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189275	0.95[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs11189278	0.86[EUR][1000 genomes]
rs11189280	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189284	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs11511362	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11528108	0.84[EUR][1000 genomes]
rs11528109	0.84[EUR][1000 genomes]
rs11814566	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12219064	0.90[CEU][hapmap]
rs12221474	0.89[CEU][hapmap]
rs12243136	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12355384	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12357750	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12415338	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12766074	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12767760	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12774288	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12775868	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779451	0.83[AMR][1000 genomes]
rs12783481	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1417408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1475757	0.81[EUR][1000 genomes]
rs1572860	0.95[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs17108059	0.85[EUR][1000 genomes]
rs2282372	0.82[CHB][hapmap]
rs3814554	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818910	0.85[CEU][hapmap]
rs4244325	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4244326	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4635019	0.86[EUR][1000 genomes]
rs4917774	0.91[CHB][hapmap]
rs4919105	0.86[CHB][hapmap]
rs4919108	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4919109	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66521603	0.82[ASN][1000 genomes]
rs68084394	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7075656	0.85[CHB][hapmap]
rs7077976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094973	0.82[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7342022	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7475470	0.86[EUR][1000 genomes]
rs7475851	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7902642	0.95[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7908668	0.83[EUR][1000 genomes]
rs7911122	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7923541	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv7508	chr10:99285375-99330501	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11189274	HOGA1	cis	lymphoblastoid	seeQTL
rs11189274	RRP12	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99303000-99327600	Weak transcription	Aorta	Aorta
2	chr10:99303200-99327600	Weak transcription	Pancreas	Pancrea
3	chr10:99303800-99327800	Weak transcription	Ovary	ovary
4	chr10:99304200-99313400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:99307200-99313600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:99308000-99313200	Weak transcription	HUVEC	blood vessel
7	chr10:99308200-99313200	Weak transcription	NHLF	lung
8	chr10:99308600-99311800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr10:99309400-99313200	Weak transcription	A549	lung
10	chr10:99309600-99313200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr10:99309800-99313000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr10:99309800-99313400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr10:99309800-99316200	Weak transcription	Liver	Liver
14	chr10:99310000-99313200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr10:99310000-99313200	Weak transcription	Adipose Nuclei	Adipose
16	chr10:99310000-99313200	Weak transcription	Fetal Stomach	stomach
17	chr10:99310000-99313200	Weak transcription	NH-A	brain
18	chr10:99310200-99313200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:99310200-99313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:99310400-99311800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr10:99310400-99312200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:99310400-99327600	Weak transcription	Lung	lung
23	chr10:99310400-99327800	Weak transcription	Right Ventricle	heart
24	chr10:99310600-99313000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr10:99310600-99313200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:99310600-99313200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:99310600-99313200	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:99310600-99313200	Weak transcription	Esophagus	oesophagus
29	chr10:99310600-99313200	Weak transcription	GM12878-XiMat	blood
30	chr10:99310600-99313200	Weak transcription	HepG2	liver
31	chr10:99310600-99313400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:99310600-99313400	Weak transcription	Right Atrium	heart
33	chr10:99310800-99312800	Weak transcription	Brain Hippocampus Middle	brain
34	chr10:99310800-99312800	Weak transcription	NHEK	skin
35	chr10:99310800-99313200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:99310800-99313200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:99310800-99313200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr10:99310800-99313200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr10:99310800-99313200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr10:99310800-99313200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:99310800-99313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:99310800-99313200	Weak transcription	Brain Angular Gyrus	brain
43	chr10:99310800-99313200	Weak transcription	Brain Anterior Caudate	brain
44	chr10:99310800-99313200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr10:99310800-99313200	Weak transcription	Brain Substantia Nigra	brain
46	chr10:99310800-99313200	Weak transcription	NHDF-Ad	bronchial
47	chr10:99310800-99313200	Weak transcription	Osteobl	bone
48	chr10:99310800-99313400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:99310800-99313400	Weak transcription	HSMMtube	muscle
50	chr10:99310800-99313600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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