Variant report

Variant	rs17030933
Chromosome Location	chr3:53290264-53290265
allele	C/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	POLR2A	chr3:53289495-53290320	ProgFib	skin:	n/a	n/a
2	STAT1	chr3:53290110-53290305	GM12878	blood:	n/a	chr3:53290175-53290187
3	BHLHE40	chr3:53289588-53290389	K562	blood:	n/a	chr3:53290199-53290215 chr3:53290149-53290165
4	POLR2A	chr3:53289470-53290415	MCF10A-Er-Src	breast:	n/a	n/a
5	EBF1	chr3:53290247-53290361	GM12878	blood:	n/a	n/a
6	MXI1	chr3:53287848-53290499	IMR90	lung:	n/a	chr3:53289133-53289142
7	POLR2A	chr3:53288604-53290552	HepG2	liver:	n/a	n/a
8	ZNF263	chr3:53290144-53290496	HEK293-T-REx	kidney:	n/a	chr3:53290306-53290327
9	GTF2F1	chr3:53290215-53290415	Hela-S3	cervix:	n/a	n/a
10	MAX	chr3:53288520-53290464	K562	blood:	n/a	chr3:53289627-53289636 chr3:53289134-53289143 chr3:53289133-53289143 chr3:53289135-53289142
11	POLR2A	chr3:53289557-53290418	K562	blood:	n/a	n/a
12	ZKSCAN1	chr3:53290257-53290455	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:53288587-53290326	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr3:53288701-53290380	GM12878	blood:	n/a	n/a
15	MAX	chr3:53288706-53290387	K562	blood:	n/a	chr3:53289627-53289636 chr3:53289134-53289143 chr3:53289133-53289143 chr3:53289135-53289142
16	HDAC2	chr3:53290131-53290435	K562	blood:	n/a	n/a
17	CTBP2	chr3:53289501-53290458	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:53288858-53290389	GM18951	blood:	n/a	n/a
19	POLR2A	chr3:53290123-53290465	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr3:53289606-53290301	Gliobla	brain:	n/a	n/a
21	TEAD4	chr3:53290078-53290513	HepG2	liver:	n/a	n/a
22	MYBL2	chr3:53290122-53290441	HepG2	liver:	n/a	n/a
23	MAX	chr3:53289783-53290554	HCT-116	colon:	n/a	n/a
24	TBP	chr3:53289796-53290458	K562	blood:	n/a	n/a
25	EP300	chr3:53289769-53290478	K562	blood:	n/a	n/a
26	RCOR1	chr3:53289497-53290572	IMR90	lung:	n/a	n/a
27	MAZ	chr3:53288771-53290366	GM12878	blood:	n/a	chr3:53289627-53289636 chr3:53289134-53289143 chr3:53289133-53289143 chr3:53289135-53289142
28	RCOR1	chr3:53290166-53290506	HepG2	liver:	n/a	n/a
29	MAX	chr3:53290228-53290387	K562	blood:	n/a	n/a
30	SP1	chr3:53289750-53290456	A549	lung:	n/a	chr3:53290145-53290154 chr3:53290145-53290154 chr3:53290144-53290156 chr3:53290144-53290156 chr3:53290305-53290319 chr3:53290179-53290188 chr3:53290146-53290155
31	BACH1	chr3:53290253-53290453	K562	blood:	n/a	n/a
32	MAFK	chr3:53290158-53290357	Hela-S3	cervix:	n/a	n/a
33	UBTF	chr3:53288609-53290369	K562	blood:	n/a	n/a
34	POLR2A	chr3:53288232-53290569	K562	blood:	n/a	n/a
35	MAX	chr3:53288631-53290518	HCT-116	colon:	n/a	chr3:53289627-53289636 chr3:53289134-53289143 chr3:53289133-53289143 chr3:53289135-53289142
36	POLR2A	chr3:53288670-53290393	GM18505	blood:	n/a	n/a
37	SMC3	chr3:53289870-53290377	Hela-S3	cervix:	n/a	chr3:53290163-53290173
38	CHD2	chr3:53289821-53290372	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:53288600-53290315	H1-hESC	embryonic stem cell:	n/a	n/a
40	REST	chr3:53289459-53290465	HL-60	blood:	n/a	n/a
41	RCOR1	chr3:53289826-53290467	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:53289326-53290364	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:53288710-53290366	K562	blood:	n/a	n/a
44	MXI1	chr3:53289535-53290341	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr3:53288520-53290278	Hela-S3	cervix:	n/a	chr3:53289133-53289142
46	POLR2A	chr3:53288813-53290285	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr3:53289605-53290264	HUVEC	blood vessel:	n/a	n/a
48	IRF1	chr3:53289827-53290405	K562	blood:	n/a	chr3:53290142-53290156
49	TAL1	chr3:53289736-53290392	K562	blood:	n/a	n/a
50	MAZ	chr3:53288803-53290376	Hela-S3	cervix:	n/a	chr3:53289627-53289636 chr3:53289134-53289143 chr3:53289133-53289143 chr3:53289135-53289142

No.	Distal block	Cell Line	Cell type
1	chr3:53287992..53290689-chr3:53381475..53383139,2	MCF-7	breast:
2	chr17:73774514..73776016-chr3:53288969..53290746,2	MCF-7	breast:
3	chr3:53268198..53270575-chr3:53287545..53290624,3	K562	blood:
4	chr3:53163023..53165298-chr3:53287497..53290275,3	K562	blood:
5	chr3:53268810..53273941-chr3:53286770..53291307,7	MCF-7	breast:
6	chr1:11968979..11971095-chr3:53288980..53290972,2	MCF-7	breast:
7	chr3:53268931..53277907-chr3:53285563..53291617,11	MCF-7	breast:
8	chr3:53288526..53291244-chr3:53879304..53881119,2	MCF-7	breast:
9	chr3:53187844..53191099-chr3:53288490..53291420,3	MCF-7	breast:

Variant related genes	Relation type
TKT	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000163931	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000163932	Chromatin interaction
ENSG00000162290	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10433617	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433618	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108506	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030934	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17234771	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235667	0.92[EUR][1000 genomes]
rs41275543	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59145995	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255993	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255994	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255999	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256000	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256003	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256009	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256043	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256049	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256050	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62256053	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256965	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256966	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256968	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256969	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62257004	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257007	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257009	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257011	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62257013	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257024	0.92[EUR][1000 genomes]
rs6780100	0.91[EUR][1000 genomes]
rs73080266	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73082274	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7622159	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830594	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830895	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846315	0.97[EUR][1000 genomes]
rs9850440	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864057	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53286400-53290400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:53286800-53290400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:53287600-53290400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:53288000-53290400	Active TSS	HSMMtube	muscle
5	chr3:53288200-53290400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:53288200-53290400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:53288400-53290400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:53288400-53290400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:53288400-53290400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:53288400-53290400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:53288400-53290400	Active TSS	HSMM	muscle
12	chr3:53288400-53290600	Active TSS	Rectal Smooth Muscle	rectum
13	chr3:53288600-53290400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:53288600-53290400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:53288600-53290400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr3:53288600-53290400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:53288600-53290400	Active TSS	NH-A	brain
18	chr3:53288600-53290400	Active TSS	Osteobl	bone
19	chr3:53288800-53290400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:53288800-53290400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:53288800-53290400	Active TSS	Primary T cells from cord blood	blood
22	chr3:53288800-53290400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:53288800-53290400	Active TSS	Ovary	ovary
24	chr3:53288800-53290600	Active TSS	Brain Anterior Caudate	brain
25	chr3:53288800-53290600	Active TSS	Fetal Kidney	kidney
26	chr3:53289000-53290400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:53289000-53290400	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr3:53289000-53290400	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:53289000-53290400	Active TSS	Brain Hippocampus Middle	brain
30	chr3:53289000-53290400	Active TSS	Fetal Lung	lung
31	chr3:53289000-53290400	Active TSS	Psoas Muscle	Psoas
32	chr3:53289000-53290400	Active TSS	Right Atrium	heart
33	chr3:53289000-53290400	Active TSS	Right Ventricle	heart
34	chr3:53289000-53290600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:53289000-53290600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:53289000-53290600	Active TSS	Brain Angular Gyrus	brain
37	chr3:53289000-53290600	Active TSS	Colonic Mucosa	Colon
38	chr3:53289000-53290600	Active TSS	Dnd41	blood
39	chr3:53289200-53290400	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr3:53289400-53290400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:53289400-53290400	Active TSS	Liver	Liver
42	chr3:53289400-53290400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:53289400-53290600	Active TSS	Brain Germinal Matrix	brain
44	chr3:53289400-53293400	Weak transcription	Fetal Heart	heart
45	chr3:53289600-53290600	Active TSS	Fetal Brain Female	brain
46	chr3:53290000-53290400	Active TSS	Primary B cells from cord blood	blood
47	chr3:53290000-53290400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:53290000-53290400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr3:53290000-53290400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:53290000-53290400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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