Variant report

Variant	rs4767478
Chromosome Location	chr12:117390339-117390340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10507277	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10507278	0.90[EUR][1000 genomes]
rs10732611	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735099	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735102	0.93[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10735103	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10744885	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10744886	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10774891	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10774892	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774893	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10774896	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10850731	0.93[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10850733	0.82[EUR][1000 genomes]
rs10850737	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10850741	0.82[EUR][1000 genomes]
rs10850743	0.93[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10850744	0.85[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap]
rs11068247	0.83[JPT][hapmap]
rs11068258	0.86[JPT][hapmap]
rs11068262	0.86[JPT][hapmap]
rs11068264	0.93[CEU][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11068277	0.93[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11068280	0.91[JPT][hapmap]
rs11068282	0.83[JPT][hapmap]
rs11068286	0.83[JPT][hapmap]
rs11068292	0.84[YRI][hapmap]
rs11068296	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11609970	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12821492	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12823620	0.86[AMR][1000 genomes]
rs17583145	0.84[JPT][hapmap]
rs17616662	0.86[JPT][hapmap]
rs2242469	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393110	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2393111	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35833140	0.85[ASN][1000 genomes]
rs3803089	0.86[JPT][hapmap]
rs3893370	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4074147	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4076700	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077519	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4130296	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4238051	0.82[EUR][1000 genomes]
rs4299000	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4324001	0.83[ASN][1000 genomes]
rs4347476	0.86[JPT][hapmap]
rs4522274	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4542506	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4562925	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4562926	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4562927	0.93[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4766812	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4766814	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766815	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766818	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766820	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4766821	0.94[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766822	0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4767473	0.82[EUR][1000 genomes]
rs4767474	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767476	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767480	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767482	0.83[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767483	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767484	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767485	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767487	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767488	0.88[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767489	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767490	0.82[EUR][1000 genomes]
rs4767491	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767493	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6490097	0.83[ASN][1000 genomes]
rs6490102	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7131746	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133066	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7136629	0.86[JPT][hapmap]
rs7137006	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137752	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297155	0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297848	0.93[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7297934	0.85[ASN][1000 genomes]
rs7298447	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303882	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308498	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308734	0.90[EUR][1000 genomes]
rs7311972	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312388	0.85[ASN][1000 genomes]
rs7316144	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73403241	0.92[EUR][1000 genomes]
rs7484620	0.89[ASN][1000 genomes]
rs7487081	1.00[JPT][hapmap]
rs7952766	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954824	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958030	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7959666	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7962339	0.87[EUR][1000 genomes]
rs7973240	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7976815	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977598	0.94[EUR][1000 genomes];0.91[ASN][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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1046811	chr12:117353904-117396230	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	esv1798657	chr12:117354067-117392259	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1048942	chr12:117365506-117400588	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	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
rs4767478	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117358400-117392600	Weak transcription	Small Intestine	intestine
2	chr12:117363200-117399400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:117365000-117406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:117373800-117393200	Weak transcription	Stomach Mucosa	stomach
5	chr12:117378000-117392600	Weak transcription	Psoas Muscle	Psoas
6	chr12:117381200-117391200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:117381600-117390400	Strong transcription	Primary T cells from cord blood	blood
8	chr12:117381600-117390800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:117381800-117390400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:117381800-117391400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:117381800-117396200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:117382000-117391400	Strong transcription	Fetal Stomach	stomach
13	chr12:117382000-117396400	Weak transcription	GM12878-XiMat	blood
14	chr12:117382400-117390400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:117382400-117390600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:117382600-117408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:117383000-117391000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:117383000-117391200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:117383000-117391400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:117383200-117390400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:117383200-117390600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:117384400-117392600	Weak transcription	Fetal Heart	heart
23	chr12:117384400-117411200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:117384600-117427400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:117384800-117393200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:117384800-117402200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:117384800-117407400	Weak transcription	Brain Angular Gyrus	brain
28	chr12:117384800-117411000	Weak transcription	Hela-S3	cervix
29	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:117385000-117393000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:117385000-117396400	Weak transcription	Colonic Mucosa	Colon
32	chr12:117385200-117399400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:117385200-117406200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:117385200-117410200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:117385200-117410600	Weak transcription	Fetal Kidney	kidney
36	chr12:117385800-117408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:117386000-117396200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:117386000-117402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:117386000-117404200	Weak transcription	HepG2	liver
40	chr12:117386000-117405000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:117386800-117390400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:117387000-117390400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:117387600-117392600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:117387600-117399800	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:117387600-117402000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:117387600-117402200	Weak transcription	Brain Substantia Nigra	brain
47	chr12:117387800-117390600	Weak transcription	Fetal Brain Male	brain
48	chr12:117387800-117392000	Weak transcription	Fetal Lung	lung
49	chr12:117387800-117392000	Weak transcription	HUVEC	blood vessel
50	chr12:117387800-117392600	Weak transcription	Brain Anterior Caudate	brain

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