Variant report

Variant	rs12466497
Chromosome Location	chr2:10074909-10074910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12477755	0.93[EUR][1000 genomes]
rs1709854	0.92[EUR][1000 genomes]
rs17364189	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241664	0.93[EUR][1000 genomes]
rs34153848	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029226	0.88[EUR][1000 genomes]
rs369551	0.90[EUR][1000 genomes]
rs369605	0.90[EUR][1000 genomes]
rs371305	0.92[EUR][1000 genomes]
rs372031	0.92[EUR][1000 genomes]
rs374197	0.92[EUR][1000 genomes]
rs375793	0.90[EUR][1000 genomes]
rs386355	0.90[EUR][1000 genomes]
rs388695	0.87[EUR][1000 genomes]
rs389002	0.88[EUR][1000 genomes]
rs391889	0.92[EUR][1000 genomes]
rs395381	0.89[EUR][1000 genomes]
rs396281	0.89[EUR][1000 genomes]
rs397498	0.90[EUR][1000 genomes]
rs397871	0.90[EUR][1000 genomes]
rs400758	0.92[EUR][1000 genomes]
rs403317	0.90[EUR][1000 genomes]
rs407874	0.89[EUR][1000 genomes]
rs408987	0.92[EUR][1000 genomes]
rs410121	0.92[EUR][1000 genomes]
rs411413	0.89[EUR][1000 genomes]
rs412039	0.90[EUR][1000 genomes]
rs414499	0.89[EUR][1000 genomes]
rs415676	0.87[EUR][1000 genomes]
rs416228	0.88[EUR][1000 genomes]
rs420122	0.90[EUR][1000 genomes]
rs421030	0.90[EUR][1000 genomes]
rs423651	0.89[EUR][1000 genomes]
rs431519	0.92[EUR][1000 genomes]
rs431562	0.90[EUR][1000 genomes]
rs437662	0.90[EUR][1000 genomes]
rs437906	0.88[EUR][1000 genomes]
rs438762	0.90[EUR][1000 genomes]
rs438966	0.92[EUR][1000 genomes]
rs439310	0.92[EUR][1000 genomes]
rs444650	0.89[EUR][1000 genomes]
rs447476	0.90[EUR][1000 genomes]
rs448287	0.90[EUR][1000 genomes]
rs449472	0.89[EUR][1000 genomes]
rs450194	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs450286	0.90[EUR][1000 genomes]
rs450643	0.90[EUR][1000 genomes]
rs451045	0.92[EUR][1000 genomes]
rs452789	0.89[EUR][1000 genomes]
rs453568	0.90[EUR][1000 genomes]
rs453933	0.90[EUR][1000 genomes]
rs454269	0.90[EUR][1000 genomes]
rs4669498	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669499	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499858	0.92[EUR][1000 genomes]
rs56010640	0.92[EUR][1000 genomes]
rs56241824	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258032	0.83[EUR][1000 genomes]
rs56382546	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs71437684	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12466497	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs12466497	RP11-95D17.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12466497	TAF1B	cis	lung	GTEx
rs12466497	TAF1B	cis	Nerve Tibial	GTEx
rs12466497	TAF1B	cis	Adipose Subcutaneous	GTEx
rs12466497	TAF1B	cis	Muscle Skeletal	GTEx
rs12466497	RP11-95D17.1	cis	Adipose Subcutaneous	GTEx
rs12466497	TAF1B	cis	Esophagus Muscularis	GTEx
rs12466497	TAF1B	cis	Artery Tibial	GTEx
rs12466497	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
3	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
11	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
13	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
14	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
15	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:10053200-10077800	Weak transcription	Liver	Liver
19	chr2:10054800-10079000	Weak transcription	Fetal Kidney	kidney
20	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
21	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:10055200-10079600	Weak transcription	K562	blood
24	chr2:10055200-10080800	Weak transcription	HMEC	breast
25	chr2:10055800-10075800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:10058800-10076000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
28	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
29	chr2:10060400-10075800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:10060600-10075200	Weak transcription	Osteobl	bone
31	chr2:10060600-10080200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:10060800-10077400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:10061000-10079600	Weak transcription	HepG2	liver
34	chr2:10061000-10080800	Weak transcription	Brain Germinal Matrix	brain
35	chr2:10061000-10080800	Weak transcription	NH-A	brain
36	chr2:10061000-10080800	Weak transcription	NHEK	skin
37	chr2:10061400-10077800	Weak transcription	Primary B cells from cord blood	blood
38	chr2:10061600-10077800	Weak transcription	Ovary	ovary
39	chr2:10062600-10080200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:10063000-10080800	Weak transcription	NHLF	lung
41	chr2:10064200-10079400	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:10064200-10080200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:10064600-10079200	Weak transcription	Fetal Brain Female	brain
44	chr2:10064800-10077000	Weak transcription	Fetal Lung	lung
45	chr2:10065000-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:10069000-10077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:10069600-10079800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:10070800-10076000	Strong transcription	Fetal Thymus	thymus
49	chr2:10070800-10080800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:10071600-10075600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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