Variant report

Variant	rs55680528
Chromosome Location	chr1:47050655-47050656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1054743	0.89[ASN][1000 genomes]
rs10890405	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211306	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211309	0.90[ASN][1000 genomes]
rs11211312	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211317	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211328	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12029680	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047046	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12048342	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12093643	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12138971	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1933934	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3753359	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766231	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766236	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766240	0.83[EUR][1000 genomes]
rs3818323	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56869893	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59446321	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429606	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7552833	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556307	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556481	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764803	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8602	0.87[EUR][1000 genomes]
rs9659890	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804164	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9804165	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55680528	MKNK1	cis	lung	GTEx
rs55680528	MOB3C	cis	Whole Blood	GTEx
rs55680528	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs55680528	MKNK1-AS1	cis	Whole Blood	GTEx
rs55680528	MKNK1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47021000-47057000	Weak transcription	Fetal Brain Male	brain
2	chr1:47021800-47054600	Weak transcription	A549	lung
3	chr1:47022400-47053600	Strong transcription	Thymus	Thymus
4	chr1:47022600-47051400	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:47022600-47051600	Strong transcription	Liver	Liver
6	chr1:47023200-47051200	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:47023800-47053200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:47024000-47054800	Weak transcription	HUVEC	blood vessel
10	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
11	chr1:47035200-47053000	Strong transcription	Spleen	Spleen
12	chr1:47035600-47053400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:47036000-47056400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:47036000-47060000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:47036400-47053200	Strong transcription	Fetal Stomach	stomach
16	chr1:47037800-47057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:47038400-47053200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:47038600-47050800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:47039000-47052600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:47039000-47054800	Weak transcription	Hela-S3	cervix
21	chr1:47039200-47053000	Weak transcription	Right Atrium	heart
22	chr1:47039200-47060400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:47039600-47052400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:47039600-47060000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:47040000-47053000	Strong transcription	Left Ventricle	heart
26	chr1:47040000-47053200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:47040200-47060400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:47040800-47053000	Strong transcription	NHEK	skin
29	chr1:47041000-47053600	Strong transcription	Aorta	Aorta
30	chr1:47041200-47052400	Strong transcription	Right Ventricle	heart
31	chr1:47041200-47053200	Strong transcription	Fetal Intestine Small	intestine
32	chr1:47041200-47054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:47041600-47053200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:47042200-47057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:47042400-47052800	Strong transcription	Colon Smooth Muscle	Colon
36	chr1:47042400-47057200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:47042600-47060400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:47042800-47052400	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:47042800-47054600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:47042800-47056600	Weak transcription	Small Intestine	intestine
42	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:47043600-47053600	Strong transcription	HMEC	breast
44	chr1:47045400-47051200	Strong transcription	Adipose Nuclei	Adipose
45	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:47046200-47056400	Weak transcription	NH-A	brain
47	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
48	chr1:47046400-47055200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:47046400-47057200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:47046600-47054800	Weak transcription	Stomach Mucosa	stomach

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