Variant report

Variant	rs12093643
Chromosome Location	chr1:47058863-47058864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10890405	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211306	0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211309	0.81[ASN][1000 genomes]
rs11211312	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211317	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211328	0.82[CEU][hapmap];0.87[ASN][1000 genomes]
rs12029680	0.82[CEU][hapmap];0.87[ASN][1000 genomes]
rs12047046	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12048342	0.90[ASN][1000 genomes]
rs12138971	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1933934	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2181414	0.83[CEU][hapmap]
rs3753359	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766231	0.82[CEU][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766236	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766240	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3818323	0.86[CEU][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55680528	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56869893	0.81[ASN][1000 genomes]
rs59446321	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6429606	0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543083	0.83[CEU][hapmap]
rs7552833	0.88[ASN][1000 genomes]
rs7556307	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7556481	0.82[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs764803	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9659890	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9804164	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9804165	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active 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	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12093643	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs12093643	MKNK1	cis	lung	GTEx
rs12093643	MKNK1	cis	Whole Blood	GTEx
rs12093643	MOB3C	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
3	chr1:47036000-47060000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr1:47039200-47060400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:47039600-47060000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:47040200-47060400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:47042600-47060400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
12	chr1:47047800-47060000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:47048400-47069000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:47049600-47060400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:47050600-47068600	Weak transcription	NHDF-Ad	bronchial
16	chr1:47051000-47061000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:47051600-47059200	Strong transcription	HepG2	liver
18	chr1:47051600-47059800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:47052200-47060000	Strong transcription	Liver	Liver
20	chr1:47052200-47060000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr1:47052400-47060000	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:47053200-47060200	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:47054400-47059000	Strong transcription	Aorta	Aorta
24	chr1:47054400-47059200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:47054400-47060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:47054400-47060000	Strong transcription	Fetal Thymus	thymus
27	chr1:47054400-47060000	Strong transcription	Lung	lung
28	chr1:47054400-47060000	Strong transcription	Thymus	Thymus
29	chr1:47054600-47059000	Strong transcription	Brain Angular Gyrus	brain
30	chr1:47054600-47059000	Strong transcription	Ovary	ovary
31	chr1:47054600-47059000	Strong transcription	Right Ventricle	heart
32	chr1:47054600-47059200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:47054600-47059200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:47054600-47059200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:47054600-47059200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:47054600-47059200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:47054600-47059200	Strong transcription	Colon Smooth Muscle	Colon
38	chr1:47054600-47059200	Strong transcription	Fetal Brain Female	brain
39	chr1:47054600-47059200	Strong transcription	Rectal Smooth Muscle	rectum
40	chr1:47054600-47059400	Strong transcription	Primary T cells from cord blood	blood
41	chr1:47054600-47059600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:47054600-47059800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:47054600-47059800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:47054600-47059800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:47054600-47059800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:47054600-47059800	Strong transcription	Adipose Nuclei	Adipose
47	chr1:47054600-47059800	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr1:47054600-47059800	Strong transcription	Gastric	stomach
49	chr1:47054600-47059800	Strong transcription	HSMMtube	muscle
50	chr1:47054600-47060000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links