Variant report

Variant	rs56306491
Chromosome Location	chr3:49314960-49314961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49313891-49315337	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:49313815-49315390	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:49313870-49315078	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr3:49313706-49315442	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:49314047-49315176	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:49314025-49314978	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:49314087-49315132	PBDE	blood:	n/a	n/a
8	STAT3	chr3:49314938-49315030	MCF10A-Er-Src	breast:	n/a	chr3:49315004-49315011
9	NFATC1	chr3:49313836-49315065	GM12878	blood:	n/a	n/a
10	PML	chr3:49313557-49315281	GM12878	blood:	n/a	chr3:49315192-49315201
11	NFIC	chr3:49314230-49314989	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:49313830-49314999	HL-60	blood:	n/a	n/a
13	POLR2A	chr3:49314139-49315008	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49314057-49315161	PANC-1	pancreas:	n/a	n/a
15	MAZ	chr3:49313736-49315010	IMR90	lung:	n/a	n/a
16	POLR2A	chr3:49313819-49315176	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:49313762-49314985	GM12891	blood:	n/a	n/a
18	MTA3	chr3:49313432-49315520	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49313890-49315407	HUVEC	blood vessel:	n/a	n/a
20	YY1	chr3:49314063-49315004	GM12891	blood:	n/a	chr3:49314463-49314471
21	EP300	chr3:49313999-49315017	ECC-1	luminal epithelium:	n/a	chr3:49314518-49314534
22	POLR2A	chr3:49313656-49315136	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:49313827-49315159	PANC-1	pancreas:	n/a	n/a
24	GATA1	chr3:49314699-49315291	PBDE	blood:	n/a	n/a
25	POLR2A	chr3:49313553-49315014	HL-60	blood:	n/a	n/a
26	POLR2A	chr3:49313767-49315147	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr3:49313878-49315082	GM12892	blood:	n/a	n/a
28	POLR2A	chr3:49313529-49315539	GM12878	blood:	n/a	n/a
29	STAT5A	chr3:49314200-49315045	GM12878	blood:	n/a	chr3:49315004-49315011
30	POLR2A	chr3:49313757-49315463	GM12878	blood:	n/a	n/a
31	NFIC	chr3:49314043-49315209	GM12878	blood:	n/a	n/a
32	NFATC1	chr3:49313773-49315142	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:49313807-49315155	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr3:49313598-49315358	GM12892	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49314920-49314970	HRPEpiC	eye:	n/a
2	chr3:49314920-49314970	K562	blood:	n/a
3	chr3:49314920-49314970	NB4	blood:	n/a
4	chr3:49314920-49314970	GM12878	blood:	n/a
5	chr3:49314920-49314970	GM12892	blood:	n/a
6	chr3:49314920-49314970	HIPEpiC	eye:	n/a
7	chr3:49314920-49314970	MCF10A-Er-Src	breast:	n/a
8	chr3:49314920-49314970	U87	brain:	n/a
9	chr3:49314920-49314970	HRCEpiC	kidney:	n/a
10	chr3:49314920-49314970	AoSMC	blood vessel:	n/a
11	chr3:49314920-49314970	CMK	blood:	n/a
12	chr3:49314920-49314970	GM06990	blood:	n/a
13	chr3:49314920-49314970	Jurkat	blood:	n/a
14	chr3:49314920-49314970	RPTEC	kidney:	n/a
15	chr3:49314920-49314970	GM12891	blood:	n/a
16	chr3:49314920-49314970	AG10803	skin:	n/a
17	chr3:49314920-49314970	AG04449	skin:	fetal
18	chr3:49314920-49314970	HAEpiC	amniotic membrane:	n/a
19	chr3:49314920-49314970	NHDF-neo	bronchial:	n/a
20	chr3:49314920-49314970	SKMC	muscle:	n/a
21	chr3:49314920-49314970	SK-N-SH_RA	brain:	n/a
22	chr3:49314920-49314970	ProgFib	skin:	n/a
23	chr3:49314920-49314970	MCF-7	breast:	n/a
24	chr3:49314920-49314970	Caco-2	colon:	n/a
25	chr3:49314920-49314970	LNCaP	prostate:	n/a
26	chr3:49314920-49314970	HepG2	liver:	n/a
27	chr3:49314920-49314970	HEK293	kidney:	embryo
28	chr3:49314920-49314970	AG09319	gingival:	n/a
29	chr3:49314920-49314970	Hepatocyte	liver:	n/a
30	chr3:49314920-49314970	T-47D	breast:	n/a
31	chr3:49314920-49314970	A549	lung:	n/a
32	chr3:49314920-49314970	HCT-116	colon:	n/a
33	chr3:49314920-49314970	HCM	heart:	n/a
34	chr3:49314920-49314970	HRE	kidney:	n/a
35	chr3:49314920-49314970	AG09309	skin:	n/a
36	chr3:49314920-49314970	NH-A	brain:	n/a
37	chr3:49314920-49314970	HL-60	blood:	n/a
38	chr3:49314920-49314970	ovcar-3	ovarian:	n/a
39	chr3:49314920-49314970	HPAEpiC	pulmonary alveolar:	n/a
40	chr3:49314920-49314970	Hela-S3	cervix:	n/a
41	chr3:49314920-49314970	HEEpiC	esophagus:	n/a
42	chr3:49314920-49314970	IMR90	lung:	fetal
43	chr3:49314920-49314970	AG04450	lung:	fetal
44	chr3:49314920-49314970	GM19239	blood:	n/a
45	chr3:49314920-49314970	SK-N-MC	brain:	n/a
46	chr3:49314920-49314970	NT2-D1	testis:	n/a
47	chr3:49314920-49314970	HCPEpiC	choroid plexus:	n/a
48	chr3:49314920-49314970	PANC-1	pancreas:	n/a
49	chr3:49314920-49314970	ECC-1	luminal epithelium:	n/a
50	chr3:49314920-49314970	HUVEC	blood vessel:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49313590..49315716-chr3:49315985..49318300,2	MCF-7	breast:
2	chr3:49227118..49229185-chr3:49314324..49316369,3	K562	blood:

No data

Variant related genes	Relation type
C3orf62	TF binding region
C3orf62	CpG island
ENSG00000236980	Chromatin interaction
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10049462	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10154895	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11552724	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706189	0.87[EUR][1000 genomes]
rs11710247	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11713297	0.87[EUR][1000 genomes]
rs11718982	0.86[EUR][1000 genomes]
rs11719220	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11720460	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12715434	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13068038	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13077498	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13096406	0.87[EUR][1000 genomes]
rs34343820	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34566463	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34784192	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35060561	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35185152	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35673421	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5030795	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55921200	0.89[AMR][1000 genomes]
rs61729488	1.00[AFR][1000 genomes]
rs66991555	0.87[EUR][1000 genomes]
rs67286839	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67831908	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71324929	1.00[AFR][1000 genomes]
rs71324939	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73084135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9311439	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9814987	0.86[EUR][1000 genomes]
rs9826525	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9828310	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9835439	0.84[EUR][1000 genomes]
rs9837237	0.87[EUR][1000 genomes]
rs9837625	0.87[EUR][1000 genomes]
rs9844757	0.89[EUR][1000 genomes]
rs9847839	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9850917	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9855123	0.87[EUR][1000 genomes]
rs9862483	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9870030	0.91[EUR][1000 genomes]
rs9880088	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9880309	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9990153	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56306491	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs56306491	WDR6	cis	Adipose Subcutaneous	GTEx
rs56306491	WDR6	cis	Esophagus Mucosa	GTEx
rs56306491	WDR6	cis	Artery Tibial	GTEx
rs56306491	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs56306491	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49301800-49315600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49303600-49315600	Weak transcription	HepG2	liver
3	chr3:49309200-49316000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:49311800-49315200	Weak transcription	K562	blood
5	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:49313200-49318600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:49313200-49326200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49313200-49349400	Strong transcription	Dnd41	blood
9	chr3:49313400-49318600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:49313600-49315000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:49313600-49315000	Active TSS	Aorta	Aorta
12	chr3:49313600-49315000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr3:49313600-49315200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:49313600-49315200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:49313600-49315200	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr3:49313600-49315200	Transcr. at gene 5' and 3'	Placenta	Placenta
17	chr3:49313600-49315200	Flanking Active TSS	HUVEC	blood vessel
18	chr3:49313600-49315200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr3:49313600-49315400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:49313600-49315400	Enhancers	Spleen	Spleen
21	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:49313800-49315000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:49313800-49315000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:49313800-49315000	Flanking Active TSS	Fetal Thymus	thymus
25	chr3:49313800-49315200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:49314000-49315000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:49314000-49315000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr3:49314000-49315000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr3:49314000-49315000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:49314000-49315000	Flanking Active TSS	Colonic Mucosa	Colon
31	chr3:49314000-49315000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr3:49314000-49315200	Flanking Active TSS	NHEK	skin
33	chr3:49314000-49315400	Active TSS	A549	lung
34	chr3:49314200-49315000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:49314200-49315000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr3:49314200-49315000	Active TSS	Brain Angular Gyrus	brain
37	chr3:49314200-49315000	Active TSS	Brain Anterior Caudate	brain
38	chr3:49314200-49315000	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:49314200-49315000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:49314200-49315000	Active TSS	Esophagus	oesophagus
41	chr3:49314200-49315000	Active TSS	Ovary	ovary
42	chr3:49314200-49315000	Active TSS	Pancreas	Pancrea
43	chr3:49314200-49315000	Active TSS	Psoas Muscle	Psoas
44	chr3:49314200-49315000	Active TSS	Rectal Smooth Muscle	rectum
45	chr3:49314200-49315000	Active TSS	Small Intestine	intestine
46	chr3:49314200-49315200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr3:49314200-49315200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:49314200-49315200	Active TSS	Fetal Muscle Trunk	muscle
49	chr3:49314200-49315200	Active TSS	Left Ventricle	heart
50	chr3:49314200-49315200	Active TSS	Right Atrium	heart

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