Variant report

Variant	rs7552833
Chromosome Location	chr1:47083025-47083026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:47081533-47083316	K562	blood:	n/a	n/a
2	RCOR1	chr1:47080951-47083959	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:47081453-47083127	Hela-S3	cervix:	n/a	n/a
4	RCOR1	chr1:47082655-47083083	K562	blood:	n/a	n/a
5	SRF	chr1:47081807-47083153	HCT-116	colon:	n/a	n/a
6	SRF	chr1:47082327-47083122	ECC-1	luminal epithelium:	n/a	n/a
7	HCFC1	chr1:47081966-47083038	K562	blood:	n/a	n/a
8	TCF12	chr1:47082126-47083107	ECC-1	luminal epithelium:	n/a	chr1:47082654-47082664
9	STAT3	chr1:47082570-47083033	MCF10A-Er-Src	breast:	n/a	chr1:47082628-47082637 chr1:47082623-47082643 chr1:47082627-47082638 chr1:47082629-47082638 chr1:47082629-47082637
10	SRF	chr1:47082345-47083214	MCF-7	breast:	n/a	n/a
11	MAX	chr1:47082300-47083121	A549	lung:	n/a	chr1:47083058-47083068
12	TBL1XR1	chr1:47082306-47083079	K562	blood:	n/a	n/a
13	GATA1	chr1:47082340-47083262	PBDE	blood:	n/a	chr1:47083122-47083131 chr1:47083119-47083129 chr1:47083121-47083131 chr1:47083122-47083129 chr1:47083118-47083134 chr1:47083122-47083129 chr1:47083122-47083129 chr1:47083115-47083136 chr1:47082799-47082806
14	JUND	chr1:47081975-47083057	K562	blood:	n/a	chr1:47082335-47082344
15	WRNIP1	chr1:47081432-47083222	GM12878	blood:	n/a	n/a
16	USF2	chr1:47082491-47083054	GM12878	blood:	n/a	n/a
17	BHLHE40	chr1:47081880-47083091	K562	blood:	n/a	n/a
18	MAZ	chr1:47081502-47083027	GM12878	blood:	n/a	n/a
19	SRF	chr1:47082302-47083028	MCF-7	breast:	n/a	n/a
20	SRF	chr1:47082213-47083301	HCT-116	colon:	n/a	n/a
21	SMARCC1	chr1:47081534-47083403	Hela-S3	cervix:	n/a	n/a
22	CTBP2	chr1:47081874-47083178	H1-hESC	embryonic stem cell:	n/a	n/a
23	TFAP2C	chr1:47082213-47083042	Hela-S3	cervix:	n/a	n/a
24	E2F6	chr1:47081630-47083195	K562	blood:	n/a	chr1:47082336-47082345
25	ELF1	chr1:47082169-47083042	GM12878	blood:	n/a	n/a
26	BCL3	chr1:47082395-47083126	A549	lung:	n/a	n/a
27	MAX	chr1:47081843-47083050	K562	blood:	n/a	n/a
28	IRF1	chr1:47081931-47083127	K562	blood:	n/a	chr1:47082317-47082331 chr1:47082316-47082327 chr1:47082315-47082329
29	POLR2A	chr1:47081384-47083061	GM12878	blood:	n/a	n/a
30	MTA3	chr1:47081339-47083135	GM12878	blood:	n/a	n/a
31	MAZ	chr1:47080667-47083935	IMR90	lung:	n/a	chr1:47083058-47083068
32	POLR2A	chr1:47081243-47083109	GM18505	blood:	n/a	n/a
33	ZC3H11A	chr1:47082455-47083231	K562	blood:	n/a	n/a
34	MAZ	chr1:47081486-47083313	K562	blood:	n/a	chr1:47083058-47083068
35	MXI1	chr1:47081458-47083082	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
2	chr1:47078421..47080865-chr1:47080975..47083544,2	MCF-7	breast:

Variant related genes	Relation type
MOB3C	TF binding region
MKNK1	TF binding region
ENSG00000079277	Chromatin interaction
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1054743	0.86[ASN][1000 genomes]
rs10890405	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211306	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211309	0.87[ASN][1000 genomes]
rs11211312	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211317	0.87[ASN][1000 genomes]
rs11211328	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12029680	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047046	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048342	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12093643	0.88[ASN][1000 genomes]
rs12138971	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1933934	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3753359	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766231	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766236	0.87[ASN][1000 genomes]
rs3818323	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55680528	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56869893	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59446321	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6429606	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556307	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556481	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764803	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8602	0.80[EUR][1000 genomes]
rs9659890	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9804164	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9804165	0.94[EUR][1000 genomes];0.88[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	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
5	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7552833	MKNK1	cis	lung	GTEx
rs7552833	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs7552833	MKNK1	cis	Whole Blood	GTEx
rs7552833	MOB3C	cis	Whole Blood	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47081800-47083200	Active TSS	HSMM	muscle
2	chr1:47081800-47083200	Active TSS	HSMMtube	muscle
3	chr1:47081800-47083400	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:47082000-47083200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:47082000-47083200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:47082000-47083200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:47082000-47083200	Active TSS	Fetal Lung	lung
8	chr1:47082000-47083200	Active TSS	NH-A	brain
9	chr1:47082000-47083200	Active TSS	NHEK	skin
10	chr1:47082600-47083200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:47082600-47083200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr1:47082600-47083200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:47082600-47083200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:47082600-47083200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:47082600-47083200	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr1:47082600-47083200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:47082600-47083200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:47082600-47083400	Flanking Active TSS	K562	blood
19	chr1:47082800-47083200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
20	chr1:47082800-47083200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr1:47082800-47083200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:47082800-47083200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr1:47082800-47083200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:47082800-47083200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:47082800-47083200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:47082800-47083200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:47082800-47083200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:47082800-47083200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:47082800-47083200	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr1:47082800-47083200	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr1:47082800-47083200	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr1:47082800-47083200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr1:47082800-47083200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr1:47082800-47083200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:47082800-47083200	Flanking Active TSS	Brain Substantia Nigra	brain
36	chr1:47082800-47083200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr1:47082800-47083200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr1:47082800-47083200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr1:47082800-47083200	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr1:47082800-47083200	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr1:47082800-47083200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr1:47082800-47083200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr1:47082800-47083200	Flanking Active TSS	A549	lung
44	chr1:47082800-47083200	Flanking Active TSS	Hela-S3	cervix
45	chr1:47082800-47083200	Flanking Active TSS	HMEC	breast
46	chr1:47082800-47083200	Flanking Active TSS	HUVEC	blood vessel
47	chr1:47082800-47083200	Flanking Active TSS	Osteobl	bone
48	chr1:47082800-47083400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:47082800-47083400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr1:47082800-47083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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