Variant report

Variant	rs3753359
Chromosome Location	chr1:47071176-47071177
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47069302-47071281	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:47069152-47071237	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:47069463-47071390	GM18505	blood:	n/a	n/a
4	POLR2A	chr1:47069428-47071324	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:47070841-47071271	HL-60	blood:	n/a	n/a
6	POLR2A	chr1:47070882-47071208	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47069390..47072755-chr1:47079314..47082367,4	MCF-7	breast:
2	chr1:47041661..47043778-chr1:47070091..47072496,2	K562	blood:
3	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
4	chr1:47069986..47078443-chr1:47078833..47084050,15	K562	blood:
5	chr1:47066512..47069474-chr1:47070954..47073416,4	K562	blood:
6	chr1:47069954..47072526-chr1:47696601..47699407,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF1-AS1-3	chr1:47070418-47071240	NONHSAT003028

No data

Variant related genes	Relation type
MKNK1	TF binding region
ENSG00000079277	Chromatin interaction
ENSG00000162367	Chromatin interaction
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1054743	0.88[ASN][1000 genomes]
rs10890405	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211306	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211309	0.89[ASN][1000 genomes]
rs11211312	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211317	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211328	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029680	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047046	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048342	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12093643	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12138971	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933934	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766231	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766236	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818323	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55680528	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56869893	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59446321	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429606	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552833	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556307	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556481	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764803	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8602	0.84[EUR][1000 genomes]
rs9659890	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9804164	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9804165	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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	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	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
4	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
rs3753359	MKNK1	cis	lung	GTEx
rs3753359	MKNK1	cis	Whole Blood	GTEx
rs3753359	MOB3C	cis	Whole Blood	GTEx
rs3753359	MKNK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47069000-47071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:47070000-47077600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:47070000-47078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47070200-47071200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr1:47070200-47071200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:47070200-47071200	Enhancers	Spleen	Spleen
7	chr1:47070200-47071200	Flanking Active TSS	Dnd41	blood
8	chr1:47070200-47073200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:47070400-47071200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:47070400-47071200	Flanking Active TSS	Thymus	Thymus
11	chr1:47070400-47072000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:47070400-47073600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:47070400-47073600	Weak transcription	Brain Substantia Nigra	brain
14	chr1:47070400-47073800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:47070400-47081200	Weak transcription	Fetal Brain Male	brain
16	chr1:47070600-47071200	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:47070600-47071200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:47070600-47071200	Enhancers	Adipose Nuclei	Adipose
19	chr1:47070600-47071200	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:47070600-47071200	Enhancers	Left Ventricle	heart
21	chr1:47070600-47071200	Enhancers	Right Atrium	heart
22	chr1:47070600-47071200	Enhancers	Right Ventricle	heart
23	chr1:47070600-47071200	Enhancers	Small Intestine	intestine
24	chr1:47070600-47071200	Enhancers	K562	blood
25	chr1:47070600-47071200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr1:47070600-47071200	Enhancers	NHDF-Ad	bronchial
27	chr1:47070600-47071400	Enhancers	Pancreas	Pancrea
28	chr1:47070600-47071400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:47070600-47071600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:47070600-47071600	Weak transcription	Fetal Stomach	stomach
31	chr1:47070600-47071800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:47070600-47072000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:47070600-47072000	Weak transcription	Osteobl	bone
34	chr1:47070600-47072200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:47070600-47072200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:47070600-47072600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:47070600-47073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:47070600-47073200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:47070600-47073200	Weak transcription	Aorta	Aorta
40	chr1:47070600-47073200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:47070600-47073200	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:47070600-47073400	Weak transcription	Fetal Intestine Large	intestine
43	chr1:47070600-47073600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:47070600-47073600	Weak transcription	Esophagus	oesophagus
45	chr1:47070600-47073600	Weak transcription	Gastric	stomach
46	chr1:47070600-47073800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:47070600-47073800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:47070600-47073800	Weak transcription	Fetal Lung	lung
49	chr1:47070600-47073800	Enhancers	Psoas Muscle	Psoas
50	chr1:47070600-47074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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