Variant report

Variant	rs11065286
Chromosome Location	chr12:121271734-121271735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1105416	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1151851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs1151860	0.85[YRI][hapmap]
rs1168945	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1168954	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1168956	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1696363	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1718211	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2454729	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2649996	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2649998	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2650006	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3844037	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4767938	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs482522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs487310	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487912	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs491602	0.81[ASN][1000 genomes]
rs493811	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs497273	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs498230	0.93[ASN][1000 genomes]
rs498255	0.91[YRI][hapmap]
rs513940	0.85[YRI][hapmap]
rs519785	0.80[YRI][hapmap]
rs520405	0.94[ASN][1000 genomes]
rs532140	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs532703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538785	0.81[ASN][1000 genomes]
rs550349	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs551087	0.90[JPT][hapmap]
rs564120	0.94[ASN][1000 genomes]
rs566994	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs581515	0.85[YRI][hapmap]
rs584001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs586305	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs589699	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs594507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs597203	0.94[ASN][1000 genomes]
rs610578	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs618849	0.80[ASN][1000 genomes]
rs619679	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs628771	0.81[ASN][1000 genomes]
rs631168	0.81[ASN][1000 genomes]
rs633084	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs639343	0.85[YRI][hapmap]
rs645661	0.85[YRI][hapmap]
rs648262	0.89[YRI][hapmap]
rs6553	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs656933	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs662284	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs662739	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs674021	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs679833	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs680303	0.94[ASN][1000 genomes]
rs683091	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs683437	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs688402	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs694303	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs708784	0.85[YRI][hapmap]
rs791210	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs791707	0.96[ASN][1000 genomes]
rs791713	0.81[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11065286	WSB2	cis	cerebellum	SCAN
rs11065286	SPPL3	cis	cerebellum	SCAN
rs11065286	SPPL3	cis	parietal	SCAN
rs11065286	P2RX4	cis	cerebellum	SCAN
rs11065286	SPPL3	cis	Adipose Subcutaneous	GTEx
rs11065286	ACADS	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121222200-121274000	Weak transcription	Lung	lung
2	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:121248800-121271800	Weak transcription	Dnd41	blood
4	chr12:121260800-121272400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:121261600-121274400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:121264600-121272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:121264800-121275000	Enhancers	Brain Hippocampus Middle	brain
8	chr12:121265200-121272000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:121265400-121273800	Enhancers	Brain Substantia Nigra	brain
10	chr12:121265400-121274200	Enhancers	Brain Angular Gyrus	brain
11	chr12:121266000-121274200	Enhancers	Brain Cingulate Gyrus	brain
12	chr12:121266400-121274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:121266600-121274000	Enhancers	Brain Anterior Caudate	brain
14	chr12:121266800-121276200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:121267200-121282800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:121267400-121272000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:121267400-121272600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr12:121267600-121274000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:121267600-121285800	Weak transcription	Colonic Mucosa	Colon
20	chr12:121267800-121274800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:121268400-121273800	Weak transcription	HSMM	muscle
22	chr12:121268400-121274000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:121268400-121274800	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:121268600-121272200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:121268600-121272600	Enhancers	Fetal Heart	heart
26	chr12:121268600-121272600	Weak transcription	NHEK	skin
27	chr12:121268600-121273200	Enhancers	Right Ventricle	heart
28	chr12:121268600-121274200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:121268600-121274600	Enhancers	Adipose Nuclei	Adipose
30	chr12:121268600-121274600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:121268600-121274800	Enhancers	Colon Smooth Muscle	Colon
32	chr12:121268600-121276200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:121268600-121276600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr12:121269000-121273600	Weak transcription	Esophagus	oesophagus
35	chr12:121269000-121273800	Weak transcription	Gastric	stomach
36	chr12:121269000-121278400	Weak transcription	Ovary	ovary
37	chr12:121269200-121272000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:121269200-121272000	Weak transcription	Placenta	Placenta
39	chr12:121269200-121272000	Weak transcription	Left Ventricle	heart
40	chr12:121269200-121272000	Weak transcription	Right Atrium	heart
41	chr12:121269200-121272000	Enhancers	A549	lung
42	chr12:121269200-121274200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:121269400-121272200	Weak transcription	Fetal Brain Male	brain
44	chr12:121269600-121272000	Weak transcription	HSMMtube	muscle
45	chr12:121269600-121272200	Weak transcription	Fetal Lung	lung
46	chr12:121269600-121274000	Weak transcription	Stomach Mucosa	stomach
47	chr12:121269600-121274200	Weak transcription	Liver	Liver
48	chr12:121269800-121272000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:121269800-121272800	Weak transcription	Fetal Brain Female	brain
50	chr12:121269800-121272800	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links