Variant report

Variant	rs300572
Chromosome Location	chr4:124320924-124320925
allele	A/G
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	CHD1	chr4:124320066-124321113	GM12878	blood:	n/a	n/a
2	CTCF	chr4:124320900-124321050	AG04450	lung:	n/a	n/a
3	CTCF	chr4:124319250-124320947	GM12878	blood:	n/a	chr4:124319836-124319854 chr4:124319818-124319831 chr4:124319842-124319851 chr4:124319838-124319851 chr4:124319841-124319854
4	RELA	chr4:124319306-124321439	GM15510	blood:	n/a	n/a
5	RAD21	chr4:124320404-124320987	A549	lung:	n/a	chr4:124320684-124320696
6	RCOR1	chr4:124320747-124321053	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:124320923-124321072	HUVEC	blood vessel:	n/a	n/a
8	RAD21	chr4:124320563-124321018	H1-hESC	embryonic stem cell:	n/a	chr4:124320684-124320696
9	POLR2A	chr4:124317591-124321155	HL-60	blood:	n/a	n/a
10	SIN3AK20	chr4:124320512-124321072	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr4:124319769-124321046	PFSK-1	brain:	n/a	n/a
12	BHLHE40	chr4:124318394-124321321	GM12878	blood:	n/a	chr4:124319567-124319583 chr4:124319731-124319747 chr4:124319756-124319772 chr4:124319602-124319618
13	CHD1	chr4:124320564-124321234	H1-hESC	embryonic stem cell:	n/a	n/a
14	MXI1	chr4:124317273-124321457	SK-N-SH	brain:	n/a	n/a
15	WRNIP1	chr4:124320444-124321040	GM12878	blood:	n/a	n/a
16	MYC	chr4:124320517-124321491	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr4:124317619-124321435	NB4	blood:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
18	STAT1	chr4:124320450-124321128	GM12878	blood:	n/a	chr4:124320862-124320876 chr4:124320977-124320989
19	RAD21	chr4:124319150-124320998	H1-hESC	embryonic stem cell:	n/a	chr4:124320215-124320227 chr4:124320059-124320073 chr4:124319838-124319848 chr4:124320684-124320696 chr4:124319837-124319850 chr4:124319842-124319855 chr4:124319836-124319848
20	RAD21	chr4:124320362-124320927	HepG2	liver:	n/a	chr4:124320684-124320696
21	ZNF143	chr4:124320509-124321045	GM12878	blood:	n/a	n/a
22	ZNF263	chr4:124317611-124321479	HEK293-T-REx	kidney:	n/a	chr4:124320581-124320590 chr4:124317910-124317931
23	TCF12	chr4:124320297-124321069	A549	lung:	n/a	n/a
24	POLR2A	chr4:124317516-124324681	PANC-1	pancreas:	n/a	n/a
25	CTCF	chr4:124320430-124321064	SK-N-SH	brain:	n/a	n/a
26	BACH1	chr4:124320560-124321032	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr4:124320900-124321050	AG09319	gingival:	n/a	n/a
28	POU2F2	chr4:124320909-124321425	GM12878	blood:	n/a	chr4:124321150-124321165 chr4:124321192-124321200 chr4:124321152-124321162 chr4:124321148-124321166 chr4:124321153-124321162 chr4:124321154-124321161
29	RAD21	chr4:124320467-124320924	ECC-1	luminal epithelium:	n/a	chr4:124320684-124320696
30	MAX	chr4:124317664-124321158	HepG2	liver:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
31	MAZ	chr4:124317421-124321556	IMR90	lung:	n/a	chr4:124319645-124319655 chr4:124319507-124319517
32	EP300	chr4:124320872-124321057	HepG2	liver:	n/a	n/a
33	POLR2A	chr4:124320554-124321025	HepG2	liver:	n/a	n/a
34	SIN3AK20	chr4:124320063-124321144	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr4:124317618-124321804	PANC-1	pancreas:	n/a	n/a
36	MXI1	chr4:124320501-124321619	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:124320597-124321689	HepG2	liver:	n/a	n/a
38	RFX5	chr4:124320613-124320936	HepG2	liver:	n/a	n/a
39	POLR2A	chr4:124317752-124321674	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr4:124317765-124321517	MCF10A-Er-Src	breast:	n/a	n/a
41	MAX	chr4:124317610-124321006	A549	lung:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
42	HEY1	chr4:124317612-124321355	HepG2	liver:	n/a	chr4:124319753-124319768 chr4:124319591-124319600 chr4:124319710-124319725 chr4:124319510-124319525
43	POLR2A	chr4:124317742-124320986	NB4	blood:	n/a	n/a
44	REST	chr4:124320420-124320997	HepG2	liver:	n/a	chr4:124320684-124320697
45	MAX	chr4:124317600-124321345	NB4	blood:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
46	SMC3	chr4:124320522-124321285	GM12878	blood:	n/a	n/a
47	TBP	chr4:124320462-124321357	HepG2	liver:	n/a	n/a
48	EP300	chr4:124320513-124321039	GM12878	blood:	n/a	chr4:124320642-124320656
49	MAX	chr4:124320545-124321198	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:124319424-124321038	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:124320912-124320962	HCF	heart:	n/a
2	chr4:124320912-124320962	K562	blood:	n/a
3	chr4:124320912-124320962	GM12891	blood:	n/a
4	chr4:124320912-124320962	GM12878	blood:	n/a
5	chr4:124320912-124320962	NT2-D1	testis:	n/a
6	chr4:124320912-124320962	NH-A	brain:	n/a
7	chr4:124320912-124320962	HCPEpiC	choroid plexus:	n/a
8	chr4:124320912-124320962	SKMC	muscle:	n/a
9	chr4:124320912-124320962	HIPEpiC	eye:	n/a
10	chr4:124320912-124320962	PANC-1	pancreas:	n/a
11	chr4:124320912-124320962	Hepatocyte	liver:	n/a
12	chr4:124320912-124320962	AG04449	skin:	fetal
13	chr4:124320912-124320962	ECC-1	luminal epithelium:	n/a
14	chr4:124320912-124320962	SAEC	small airway:	n/a
15	chr4:124320912-124320962	ProgFib	skin:	n/a
16	chr4:124320912-124320962	HRCEpiC	kidney:	n/a
17	chr4:124320912-124320962	HCM	heart:	n/a
18	chr4:124320912-124320962	HRE	kidney:	n/a
19	chr4:124320912-124320962	AoSMC	blood vessel:	n/a
20	chr4:124320912-124320962	GM06990	blood:	n/a
21	chr4:124320912-124320962	HPAEpiC	pulmonary alveolar:	n/a
22	chr4:124320912-124320962	SK-N-MC	brain:	n/a
23	chr4:124320912-124320962	SK-N-SH	brain:	n/a
24	chr4:124320912-124320962	HNPCEpiC	eye:	n/a
25	chr4:124320912-124320962	NHBE	bronchial:	n/a
26	chr4:124320912-124320962	Caco-2	colon:	n/a
27	chr4:124320912-124320962	Jurkat	blood:	n/a
28	chr4:124320912-124320962	T-47D	breast:	n/a
29	chr4:124320912-124320962	HMEC	breast:	n/a
30	chr4:124320912-124320962	RPTEC	kidney:	n/a
31	chr4:124320912-124320962	HCT-116	colon:	n/a
32	chr4:124320912-124320962	A549	lung:	n/a
33	chr4:124320912-124320962	NB4	blood:	n/a
34	chr4:124320912-124320962	IMR90	lung:	fetal
35	chr4:124320912-124320962	MCF-7	breast:	n/a
36	chr4:124320912-124320962	ovcar-3	ovarian:	n/a
37	chr4:124320912-124320962	LNCaP	prostate:	n/a
38	chr4:124320912-124320962	GM19239	blood:	n/a
39	chr4:124320912-124320962	AG04450	lung:	fetal
40	chr4:124320912-124320962	HL-60	blood:	n/a
41	chr4:124320912-124320962	Hela-S3	cervix:	n/a
42	chr4:124320912-124320962	BE2_C	brain:	n/a
43	chr4:124320912-124320962	HEK293	kidney:	embryo
44	chr4:124320912-124320962	SK-N-SH_RA	brain:	n/a
45	chr4:124320912-124320962	HepG2	liver:	n/a
46	chr4:124320912-124320962	NHDF-neo	bronchial:	n/a
47	chr4:124320912-124320962	HEEpiC	esophagus:	n/a
48	chr4:124320912-124320962	PFSK-1	brain:	n/a
49	chr4:124320912-124320962	U87	brain:	n/a
50	chr4:124320912-124320962	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:124318366..124320000-chr4:124320399..124322395,2	MCF-7	breast:
2	chr4:124317259..124319394-chr4:124319799..124323152,4	MCF-7	breast:

Variant related genes	Relation type
SPRY1	TF binding region
SPRY1	CpG island
ENSG00000164056	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10518414	0.90[ASN][1000 genomes]
rs11098709	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13145927	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13150612	0.96[ASN][1000 genomes]
rs188513	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28477228	0.96[ASN][1000 genomes]
rs28514996	0.96[ASN][1000 genomes]
rs300555	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs300573	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs300574	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833277	0.96[ASN][1000 genomes]
rs4833278	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9992811	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006945	chr4:124206328-124503863	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv537240	chr4:124206328-124503863	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs300572	KIAA1109	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124317000-124322000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:124317200-124323000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:124317400-124321200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr4:124317400-124321400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:124317400-124321600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr4:124317400-124321800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:124317400-124322000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:124317400-124322200	Active TSS	Adipose Nuclei	Adipose
9	chr4:124317400-124322200	Active TSS	Fetal Kidney	kidney
10	chr4:124317400-124322200	Active TSS	Fetal Lung	lung
11	chr4:124317400-124322400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:124317400-124322400	Active TSS	Brain Anterior Caudate	brain
13	chr4:124317400-124322400	Active TSS	Fetal Intestine Large	intestine
14	chr4:124317400-124322400	Active TSS	Stomach Smooth Muscle	stomach
15	chr4:124317400-124322600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr4:124317400-124322600	Active TSS	Colon Smooth Muscle	Colon
17	chr4:124317400-124322600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr4:124317400-124322600	Active TSS	Psoas Muscle	Psoas
19	chr4:124317400-124322800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:124317400-124322800	Active TSS	Aorta	Aorta
21	chr4:124317400-124322800	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:124317400-124322800	Active TSS	NHLF	lung
23	chr4:124317400-124323200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:124317400-124327000	Active TSS	Right Atrium	heart
25	chr4:124317600-124321000	Active TSS	Hela-S3	cervix
26	chr4:124317600-124321200	Active TSS	Fetal Heart	heart
27	chr4:124317600-124321200	Flanking Bivalent TSS/Enh	Dnd41	blood
28	chr4:124317600-124321400	Active TSS	A549	lung
29	chr4:124317600-124321600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr4:124317600-124321600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr4:124317600-124321600	Active TSS	Brain Angular Gyrus	brain
32	chr4:124317600-124321600	Active TSS	Brain Cingulate Gyrus	brain
33	chr4:124317600-124321600	Active TSS	Colonic Mucosa	Colon
34	chr4:124317600-124321600	Active TSS	HSMM	muscle
35	chr4:124317600-124321800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr4:124317600-124321800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:124317600-124321800	Active TSS	Stomach Mucosa	stomach
38	chr4:124317600-124322000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr4:124317600-124322000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:124317600-124322000	Active TSS	Fetal Thymus	thymus
41	chr4:124317600-124322000	Active TSS	Ovary	ovary
42	chr4:124317600-124322200	Active TSS	NHDF-Ad	bronchial
43	chr4:124317600-124322400	Active TSS	HSMMtube	muscle
44	chr4:124317600-124322600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr4:124317600-124322600	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr4:124317600-124322600	Active TSS	Brain Hippocampus Middle	brain
47	chr4:124317600-124322600	Active TSS	Left Ventricle	heart
48	chr4:124317600-124322600	Active TSS	Thymus	Thymus
49	chr4:124317600-124322800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:124317600-124322800	Active TSS	Duodenum Mucosa	Duodenum

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