Variant report

Variant	rs56869893
Chromosome Location	chr1:47082513-47082514
allele	C/T
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	POLR2A	chr1:47082215-47082797	MCF-7	breast:	n/a	n/a
2	PAX5	chr1:47081838-47082561	GM12878	blood:	n/a	n/a
3	RCOR1	chr1:47081533-47083316	K562	blood:	n/a	n/a
4	IRF1	chr1:47081912-47082794	K562	blood:	n/a	chr1:47082317-47082331 chr1:47082316-47082327 chr1:47082315-47082329
5	POLR2A	chr1:47082191-47082560	HepG2	liver:	n/a	n/a
6	YY1	chr1:47082173-47082639	GM12892	blood:	n/a	chr1:47082340-47082354
7	USF2	chr1:47082505-47082925	Hela-S3	cervix:	n/a	n/a
8	CEBPD	chr1:47082181-47082773	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:47082212-47082546	HepG2	liver:	n/a	n/a
10	RAD21	chr1:47082419-47082783	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr1:47082194-47082843	HepG2	liver:	n/a	n/a
12	NR2F2	chr1:47082116-47082719	MCF-7	breast:	n/a	n/a
13	USF1	chr1:47082287-47082759	ECC-1	luminal epithelium:	n/a	n/a
14	E2F6	chr1:47082013-47082644	H1-hESC	embryonic stem cell:	n/a	chr1:47082336-47082345
15	POLR2A	chr1:47081652-47082834	K562	blood:	n/a	n/a
16	TAF1	chr1:47082174-47082853	PFSK-1	brain:	n/a	n/a
17	TAF1	chr1:47082177-47082694	GM12878	blood:	n/a	n/a
18	MXI1	chr1:47082209-47082741	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:47081962-47082792	MCF-7	breast:	n/a	n/a
20	RCOR1	chr1:47080951-47083959	IMR90	lung:	n/a	n/a
21	POLR2A	chr1:47081453-47083127	Hela-S3	cervix:	n/a	n/a
22	BCLAF1	chr1:47082163-47082843	GM12878	blood:	n/a	n/a
23	MYC	chr1:47081991-47082859	MCF10A-Er-Src	breast:	n/a	n/a
24	MYC	chr1:47081928-47082984	K562	blood:	n/a	n/a
25	POLR2A	chr1:47081887-47082904	GM18526	blood:	n/a	n/a
26	CBX3	chr1:47081882-47082932	K562	blood:	n/a	n/a
27	POLR2A	chr1:47082174-47082825	GM12878	blood:	n/a	n/a
28	HMGN3	chr1:47081930-47082688	K562	blood:	n/a	n/a
29	MYBL2	chr1:47082206-47082555	HepG2	liver:	n/a	n/a
30	RCOR1	chr1:47081949-47082865	GM12878	blood:	n/a	n/a
31	YY1	chr1:47082255-47082801	GM12878	blood:	n/a	chr1:47082340-47082354
32	POLR2A	chr1:47082216-47082834	Raji	blood:	n/a	n/a
33	SRF	chr1:47082388-47082823	K562	blood:	n/a	n/a
34	ELK4	chr1:47082332-47082941	Hela-S3	cervix:	n/a	n/a
35	TBP	chr1:47082287-47082651	HepG2	liver:	n/a	n/a
36	STAT1	chr1:47081878-47082815	GM12878	blood:	n/a	chr1:47082628-47082637 chr1:47082315-47082326 chr1:47082623-47082643 chr1:47082629-47082638 chr1:47082629-47082637
37	SMARCB1	chr1:47081719-47082955	Hela-S3	cervix:	n/a	n/a
38	EGR1	chr1:47082433-47082759	K562	blood:	n/a	chr1:47082614-47082628 chr1:47082617-47082627
39	POLR2A	chr1:47082161-47082771	Hela-S3	cervix:	n/a	n/a
40	MAX	chr1:47082021-47082894	HepG2	liver:	n/a	n/a
41	ZBTB7A	chr1:47081864-47082758	K562	blood:	n/a	n/a
42	POLR2A	chr1:47082171-47082613	GM12892	blood:	n/a	n/a
43	IRF1	chr1:47081961-47082819	K562	blood:	n/a	chr1:47082317-47082331 chr1:47082316-47082327 chr1:47082315-47082329
44	SRF	chr1:47081807-47083153	HCT-116	colon:	n/a	n/a
45	SRF	chr1:47082327-47083122	ECC-1	luminal epithelium:	n/a	n/a
46	ZNF143	chr1:47081941-47082842	Hela-S3	cervix:	n/a	n/a
47	MYC	chr1:47082232-47082645	MCF-7	breast:	n/a	n/a
48	SIN3AK20	chr1:47082177-47082738	PANC-1	pancreas:	n/a	n/a
49	ZBTB7A	chr1:47081858-47082896	ECC-1	luminal epithelium:	n/a	n/a
50	ELK1	chr1:47081418-47082916	GM12878	blood:	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
ENSG00000079277	Chromatin interaction
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10890405	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211306	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211312	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211328	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12029680	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047046	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12048342	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12093643	0.81[ASN][1000 genomes]
rs12138971	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933934	0.80[EUR][1000 genomes]
rs3753359	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766231	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818323	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55680528	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59446321	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6429606	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552833	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7556307	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7556481	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9659890	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9804164	0.83[EUR][1000 genomes]
rs9804165	0.83[EUR][1000 genomes];0.81[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
rs56869893	MOB3C	cis	Whole Blood	GTEx
rs56869893	MKNK1	cis	lung	GTEx
rs56869893	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs56869893	MKNK1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47081200-47083000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:47081400-47082800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:47081400-47083000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:47081600-47082600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:47081600-47082800	Active TSS	Colon Smooth Muscle	Colon
6	chr1:47081600-47082800	Active TSS	Gastric	stomach
7	chr1:47081600-47083000	Active TSS	Aorta	Aorta
8	chr1:47081600-47083000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr1:47081600-47083000	Bivalent/Poised TSS	Fetal Brain Female	brain
10	chr1:47081600-47083000	Active TSS	Ovary	ovary
11	chr1:47081600-47083000	Active TSS	NHDF-Ad	bronchial
12	chr1:47081800-47082600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:47081800-47082600	Active TSS	GM12878-XiMat	blood
14	chr1:47081800-47082800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:47081800-47082800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:47081800-47082800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:47081800-47082800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:47081800-47082800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:47081800-47082800	Active TSS	Esophagus	oesophagus
20	chr1:47081800-47082800	Active TSS	Lung	lung
21	chr1:47081800-47082800	Active TSS	Pancreas	Pancrea
22	chr1:47081800-47082800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr1:47081800-47082800	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr1:47081800-47082800	Active TSS	Small Intestine	intestine
25	chr1:47081800-47082800	Active TSS	HMEC	breast
26	chr1:47081800-47083000	Active TSS	Stomach Mucosa	stomach
27	chr1:47081800-47083000	Active TSS	NHLF	lung
28	chr1:47081800-47083200	Active TSS	HSMM	muscle
29	chr1:47081800-47083200	Active TSS	HSMMtube	muscle
30	chr1:47081800-47083400	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:47082000-47082600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:47082000-47082600	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:47082000-47082600	Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:47082000-47082600	Active TSS	Primary B cells from peripheral blood	blood
35	chr1:47082000-47082600	Active TSS	Primary T cells fromperipheralblood	blood
36	chr1:47082000-47082600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:47082000-47082600	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:47082000-47082600	Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr1:47082000-47082600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr1:47082000-47082600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:47082000-47082600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:47082000-47082600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:47082000-47082600	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:47082000-47082600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:47082000-47082600	Active TSS	Liver	Liver
46	chr1:47082000-47082600	Active TSS	Brain Germinal Matrix	brain
47	chr1:47082000-47082600	Enhancers	Fetal Brain Male	brain
48	chr1:47082000-47082600	Active TSS	Fetal Muscle Trunk	muscle
49	chr1:47082000-47082600	Active TSS	Fetal Stomach	stomach
50	chr1:47082000-47082600	Active TSS	Fetal Thymus	thymus

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