Variant report

Variant	rs4767477
Chromosome Location	chr12:117390149-117390150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10735100	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10735101	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10735102	0.93[ASW][hapmap]
rs10774895	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774898	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10850730	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10850734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10850742	0.93[EUR][1000 genomes]
rs10850747	0.83[JPT][hapmap]
rs10850751	0.88[JPT][hapmap]
rs11068264	0.86[ASW][hapmap]
rs11068276	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068277	0.81[ASW][hapmap]
rs11068292	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11068296	0.87[ASW][hapmap]
rs11834817	0.88[JPT][hapmap]
rs1472523	0.88[JPT][hapmap]
rs2062528	0.94[JPT][hapmap]
rs2173654	0.94[JPT][hapmap]
rs2291916	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2393111	0.81[ASW][hapmap]
rs2393113	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4076700	0.81[ASW][hapmap]
rs4562927	0.93[ASW][hapmap]
rs4766815	0.93[ASW][hapmap]
rs4766816	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4766823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767474	0.93[ASW][hapmap]
rs4767484	0.93[ASW][hapmap]
rs4767486	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767489	0.93[ASW][hapmap]
rs6490103	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6490106	0.83[JPT][hapmap]
rs7133090	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297303	0.88[JPT][hapmap]
rs7297848	0.87[ASW][hapmap]
rs7302127	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs7486428	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7487081	0.83[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs7958680	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7962875	0.91[EUR][1000 genomes]
rs7964668	0.88[JPT][hapmap]
rs9634171	0.94[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4767477	TESC	cis	lymphoblastoid	seeQTL
rs4767477	C12orf49	cis	parietal	SCAN
rs4767477	TESC	cis	parietal	SCAN

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	chr12:117381200-117390200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:117381200-117391200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:117381600-117390200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:117381600-117390400	Strong transcription	Primary T cells from cord blood	blood
10	chr12:117381600-117390800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:117381800-117390200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr12:117381800-117390400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:117381800-117391400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:117381800-117396200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:117382000-117391400	Strong transcription	Fetal Stomach	stomach
16	chr12:117382000-117396400	Weak transcription	GM12878-XiMat	blood
17	chr12:117382400-117390400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:117382400-117390600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:117382600-117408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:117382800-117390200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:117383000-117390200	Strong transcription	Adipose Nuclei	Adipose
22	chr12:117383000-117391000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:117383000-117391200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:117383000-117391400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:117383200-117390200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:117383200-117390200	Strong transcription	Liver	Liver
27	chr12:117383200-117390400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:117383200-117390600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:117384400-117392600	Weak transcription	Fetal Heart	heart
30	chr12:117384400-117411200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:117384600-117427400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:117384800-117393200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:117384800-117402200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:117384800-117407400	Weak transcription	Brain Angular Gyrus	brain
35	chr12:117384800-117411000	Weak transcription	Hela-S3	cervix
36	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:117385000-117393000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:117385000-117396400	Weak transcription	Colonic Mucosa	Colon
39	chr12:117385200-117399400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:117385200-117406200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:117385200-117410200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:117385200-117410600	Weak transcription	Fetal Kidney	kidney
43	chr12:117385800-117408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:117386000-117396200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:117386000-117402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:117386000-117404200	Weak transcription	HepG2	liver
47	chr12:117386000-117405000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:117386800-117390400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:117387000-117390200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr12:117387000-117390400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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