Variant report

Variant	rs11189275
Chromosome Location	chr10:99312538-99312539
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99312057..99313792-chr10:99332151..99333751,2	MCF-7	breast:
2	chr10:99203371..99205386-chr10:99311046..99312878,2	K562	blood:
3	chr10:99311940..99314624-chr10:99329998..99332096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165887	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10748698	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748700	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882956	0.89[ASN][1000 genomes]
rs10882957	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10882959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882961	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882963	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs10882965	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882966	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1107517	0.81[EUR][1000 genomes]
rs1107518	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11189244	0.88[MEX][hapmap]
rs11189245	0.82[MEX][hapmap]
rs11189253	0.82[CHB][hapmap]
rs11189259	0.82[MEX][hapmap]
rs11189266	0.89[ASN][1000 genomes]
rs11189270	0.85[EUR][1000 genomes]
rs11189274	0.95[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs11189278	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189281	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs11189284	0.90[CEU][hapmap]
rs11511362	0.85[EUR][1000 genomes]
rs11528108	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11528109	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11814566	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs12219064	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221474	0.92[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12243136	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12415338	0.84[EUR][1000 genomes]
rs12766074	0.84[EUR][1000 genomes]
rs12774288	0.80[EUR][1000 genomes]
rs12775868	0.81[EUR][1000 genomes]
rs12783481	0.85[EUR][1000 genomes]
rs1417408	0.95[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1475757	0.80[ASN][1000 genomes]
rs1572860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108059	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282373	0.80[CEU][hapmap]
rs3814554	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs3818910	0.90[CEU][hapmap]
rs4635019	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919104	0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs4919108	0.85[EUR][1000 genomes]
rs4919109	0.81[EUR][1000 genomes]
rs7077211	0.95[ASN][1000 genomes]
rs7077976	0.85[EUR][1000 genomes]
rs7089060	0.83[CHB][hapmap]
rs7094973	0.85[CEU][hapmap];0.80[GIH][hapmap]
rs7342022	0.88[EUR][1000 genomes]
rs7475470	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475851	0.84[EUR][1000 genomes]
rs7893335	0.88[MEX][hapmap]
rs7902642	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7921278	0.89[ASN][1000 genomes]
rs7921505	0.89[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11189275	C10orf28	cis	cerebellum	SCAN
rs11189275	HOGA1	cis	lymphoblastoid	seeQTL
rs11189275	WNT8B	cis	cerebellum	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	chr10:99309400-99313200	Weak transcription	A549	lung
9	chr10:99309600-99313200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr10:99309800-99313000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr10:99309800-99313400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr10:99309800-99316200	Weak transcription	Liver	Liver
13	chr10:99310000-99313200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr10:99310000-99313200	Weak transcription	Adipose Nuclei	Adipose
15	chr10:99310000-99313200	Weak transcription	Fetal Stomach	stomach
16	chr10:99310000-99313200	Weak transcription	NH-A	brain
17	chr10:99310200-99313200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:99310200-99313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:99310400-99327600	Weak transcription	Lung	lung
20	chr10:99310400-99327800	Weak transcription	Right Ventricle	heart
21	chr10:99310600-99313000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr10:99310600-99313200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:99310600-99313200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:99310600-99313200	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:99310600-99313200	Weak transcription	Esophagus	oesophagus
26	chr10:99310600-99313200	Weak transcription	GM12878-XiMat	blood
27	chr10:99310600-99313200	Weak transcription	HepG2	liver
28	chr10:99310600-99313400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:99310600-99313400	Weak transcription	Right Atrium	heart
30	chr10:99310800-99312800	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:99310800-99312800	Weak transcription	NHEK	skin
32	chr10:99310800-99313200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:99310800-99313200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:99310800-99313200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr10:99310800-99313200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr10:99310800-99313200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr10:99310800-99313200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:99310800-99313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:99310800-99313200	Weak transcription	Brain Angular Gyrus	brain
40	chr10:99310800-99313200	Weak transcription	Brain Anterior Caudate	brain
41	chr10:99310800-99313200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr10:99310800-99313200	Weak transcription	Brain Substantia Nigra	brain
43	chr10:99310800-99313200	Weak transcription	NHDF-Ad	bronchial
44	chr10:99310800-99313200	Weak transcription	Osteobl	bone
45	chr10:99310800-99313400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:99310800-99313400	Weak transcription	HSMMtube	muscle
47	chr10:99310800-99313600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr10:99310800-99313600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:99310800-99320600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr10:99310800-99326400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links