Variant report

Variant	rs72971026
Chromosome Location	chr3:119813377-119813378
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	ATF2	chr3:119812342-119815042	GM12878	blood:	n/a	n/a
2	PML	chr3:119813040-119813436	K562	blood:	n/a	n/a
3	POLR2A	chr3:119812666-119815257	HEK293	kidney:	n/a	n/a
4	SPI1	chr3:119812848-119813444	GM12891	blood:	n/a	n/a
5	SPI1	chr3:119812163-119814872	HL-60	blood:	n/a	n/a
6	GABPA	chr3:119812485-119813444	SK-N-SH	brain:	n/a	chr3:119813404-119813413
7	POLR2A	chr3:119812579-119814951	Hela-S3	cervix:	n/a	n/a
8	SPI1	chr3:119812911-119813562	HL-60	blood:	n/a	n/a
9	HA-E2F1	chr3:119813265-119814948	MCF-7	breast:	n/a	chr3:119814005-119814014 chr3:119813998-119814008 chr3:119813401-119813410 chr3:119813486-119813495 chr3:119813675-119813684
10	YY1	chr3:119812534-119813444	SK-N-SH	brain:	n/a	chr3:119813179-119813193 chr3:119813401-119813410 chr3:119813302-119813316 chr3:119813177-119813188 chr3:119813307-119813318 chr3:119813399-119813413 chr3:119812933-119812947
11	EBF1	chr3:119812519-119814796	GM12878	blood:	n/a	n/a
12	TCF12	chr3:119812183-119815169	A549	lung:	n/a	n/a
13	ZNF143	chr3:119813205-119814926	K562	blood:	n/a	chr3:119813420-119813438 chr3:119813395-119813405 chr3:119813403-119813413
14	POLR2A	chr3:119812597-119815213	Raji	blood:	n/a	n/a
15	POLR2A	chr3:119812621-119815043	GM19193	blood:	n/a	n/a
16	POLR2A	chr3:119811683-119815493	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:119812046-119815097	PBDE	blood:	n/a	n/a
18	MAX	chr3:119813029-119814903	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr3:119812657-119814857	K562	blood:	n/a	n/a
20	UBTF	chr3:119812102-119813429	K562	blood:	n/a	n/a
21	EP300	chr3:119812514-119814943	ECC-1	luminal epithelium:	n/a	chr3:119812933-119812949 chr3:119814070-119814086 chr3:119813404-119813413 chr3:119812799-119812815 chr3:119812934-119812950 chr3:119813999-119814008 chr3:119814849-119814863 chr3:119812930-119812946
22	MAZ	chr3:119811823-119815143	GM12878	blood:	n/a	chr3:119812593-119812612
23	POLR2A	chr3:119812529-119815276	HCT-116	colon:	n/a	n/a
24	RFX5	chr3:119812846-119815112	GM12878	blood:	n/a	chr3:119814006-119814015 chr3:119813079-119813094 chr3:119813666-119813674 chr3:119813487-119813496 chr3:119813036-119813052 chr3:119813676-119813685 chr3:119813933-119813942
25	POLR2A	chr3:119812680-119815142	K562	blood:	n/a	n/a
26	PML	chr3:119812706-119813523	MCF-7	breast:	n/a	n/a
27	JUND	chr3:119812614-119814906	K562	blood:	n/a	chr3:119813677-119813686 chr3:119814052-119814061 chr3:119813932-119813941
28	HEY1	chr3:119812623-119813381	K562	blood:	n/a	chr3:119813098-119813113
29	POLR2A	chr3:119812646-119813502	K562	blood:	n/a	n/a
30	TAF1	chr3:119812663-119813460	HepG2	liver:	n/a	n/a
31	TBP	chr3:119813219-119815027	HepG2	liver:	n/a	n/a
32	E2F4	chr3:119813289-119814768	MCF10A-Er-Src	breast:	n/a	chr3:119814005-119814014 chr3:119813998-119814008 chr3:119813401-119813410 chr3:119813486-119813495 chr3:119813675-119813684
33	CREB1	chr3:119813138-119814912	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr3:119813355-119813392	HepG2	liver:	n/a	n/a
35	TAF1	chr3:119812497-119814966	ECC-1	luminal epithelium:	n/a	n/a
36	YY1	chr3:119812391-119815069	SK-N-SH	brain:	n/a	chr3:119813179-119813193 chr3:119813997-119814006 chr3:119813401-119813410 chr3:119814000-119814009 chr3:119813302-119813316 chr3:119813177-119813188 chr3:119813307-119813318 chr3:119813399-119813413 chr3:119812933-119812947
37	HEY1	chr3:119812557-119814979	HepG2	liver:	n/a	chr3:119813391-119813406 chr3:119813098-119813113
38	IRF1	chr3:119813182-119814904	K562	blood:	n/a	chr3:119813675-119813684
39	EP300	chr3:119813198-119814978	GM12878	blood:	n/a	chr3:119814070-119814086 chr3:119813404-119813413 chr3:119813999-119814008 chr3:119814849-119814863
40	MYBL2	chr3:119813118-119815086	HepG2	liver:	n/a	n/a
41	TAF1	chr3:119812603-119814977	MCF-7	breast:	n/a	n/a
42	MAX	chr3:119812526-119815100	MCF-7	breast:	n/a	chr3:119812593-119812612
43	POLR2A	chr3:119812204-119815123	K562	blood:	n/a	n/a
44	POLR2A	chr3:119811867-119815267	HUVEC	blood vessel:	n/a	n/a
45	NRF1	chr3:119813188-119813464	K562	blood:	n/a	chr3:119813404-119813413 chr3:119813307-119813318
46	POLR2A	chr3:119812509-119815211	ProgFib	skin:	n/a	n/a
47	TAF1	chr3:119812471-119813606	ECC-1	luminal epithelium:	n/a	n/a
48	TBL1XR1	chr3:119813358-119813815	K562	blood:	n/a	n/a
49	MAX	chr3:119813318-119813475	HepG2	liver:	n/a	n/a
50	EP300	chr3:119812945-119813440	GM12878	blood:	n/a	chr3:119813404-119813413

No.	Distal block	Cell Line	Cell type
1	chr3:119813097..119813762-chr6:134495378..134495938,2	Hela-S3	cervix:
2	chr3:119810967..119815661-chr3:120066752..120069801,5	K562	blood:
3	chr3:119812158..119817554-chr3:119829250..119832588,6	K562	blood:
4	chr1:205600495..205601295-chr3:119812865..119813382,2	Hela-S3	cervix:
5	chr3:119812996..119815585-chrX:153772819..153775165,2	MCF-7	breast:
6	chr3:119759351..119761475-chr3:119811751..119814563,3	MCF-7	breast:
7	chr3:119186368..119188700-chr3:119811867..119814798,2	K562	blood:
8	chr3:119758303..119760523-chr3:119813063..119815758,2	K562	blood:
9	chr3:119811613..119814505-chr3:119840328..119842148,2	MCF-7	breast:
10	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
11	chr3:119812799..119816595-chr3:119829619..119835566,15	MCF-7	breast:
12	chr3:119811895..119815177-chr3:120067061..120069801,4	K562	blood:
13	chr3:119745451..119747987-chr3:119811711..119814390,2	MCF-7	breast:
14	chr3:119813314..119815193-chr3:120066557..120069483,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-1	chr3:119813266-119819259	NONHSAT091417

Variant related genes	Relation type
GSK3B	TF binding region
ENSG00000242622	TF binding region
ENSG00000241546	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000239835	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000244308	Chromatin interaction
ENSG00000163428	Chromatin interaction
ENSG00000118515	Chromatin interaction
ENSG00000158711	Chromatin interaction
ENSG00000244139	Chromatin interaction
ENSG00000240661	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000160211	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs57512425	0.92[AFR][1000 genomes]
rs58321096	0.83[AFR][1000 genomes]
rs58533045	0.84[AFR][1000 genomes]
rs72967152	0.92[AFR][1000 genomes]
rs72967170	0.92[AFR][1000 genomes]
rs72967181	0.84[AFR][1000 genomes]
rs72967186	0.84[AFR][1000 genomes]
rs72967195	0.84[AFR][1000 genomes]
rs72969103	1.00[AFR][1000 genomes]
rs72969111	1.00[AFR][1000 genomes]
rs72969116	0.92[AFR][1000 genomes]
rs72969128	1.00[AFR][1000 genomes]
rs72969131	1.00[AFR][1000 genomes]
rs72969142	1.00[AFR][1000 genomes]
rs72969149	1.00[AFR][1000 genomes]
rs72969170	1.00[AFR][1000 genomes]
rs72971013	1.00[AFR][1000 genomes]
rs72971017	1.00[AFR][1000 genomes]
rs72971018	1.00[AFR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119808000-119814800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:119808000-119816400	Active TSS	Fetal Brain Female	brain
3	chr3:119808200-119814800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:119808200-119815000	Active TSS	HMEC	breast
5	chr3:119808400-119815600	Active TSS	GM12878-XiMat	blood
6	chr3:119808600-119814800	Active TSS	NHEK	skin
7	chr3:119808800-119815000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:119808800-119815600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:119809000-119815000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:119809000-119816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:119809200-119814800	Active TSS	Brain Angular Gyrus	brain
12	chr3:119809200-119814800	Active TSS	NH-A	brain
13	chr3:119809200-119815000	Active TSS	HSMMtube	muscle
14	chr3:119809200-119815400	Active TSS	Psoas Muscle	Psoas
15	chr3:119809200-119815400	Active TSS	Right Ventricle	heart
16	chr3:119809200-119815600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:119809200-119815600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr3:119809200-119815800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:119809200-119816000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr3:119809200-119816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:119809400-119814800	Active TSS	Stomach Smooth Muscle	stomach
22	chr3:119809400-119815000	Active TSS	Fetal Thymus	thymus
23	chr3:119809400-119815000	Active TSS	Ovary	ovary
24	chr3:119809400-119815200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:119809400-119815400	Active TSS	Aorta	Aorta
26	chr3:119809400-119815600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:119809400-119815800	Active TSS	HSMM	muscle
28	chr3:119809400-119816000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr3:119809600-119814800	Active TSS	Colonic Mucosa	Colon
30	chr3:119809600-119814800	Active TSS	Fetal Kidney	kidney
31	chr3:119809600-119814800	Active TSS	Fetal Stomach	stomach
32	chr3:119809600-119815000	Active TSS	Fetal Intestine Large	intestine
33	chr3:119809600-119815000	Active TSS	Fetal Lung	lung
34	chr3:119809600-119815000	Active TSS	Fetal Muscle Leg	muscle
35	chr3:119809600-119815200	Active TSS	Left Ventricle	heart
36	chr3:119809600-119815400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:119809600-119815600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:119809600-119815800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:119809600-119815800	Active TSS	NHLF	lung
40	chr3:119809600-119816000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr3:119809800-119814800	Active TSS	Primary T cells fromperipheralblood	blood
42	chr3:119809800-119814800	Active TSS	Brain Anterior Caudate	brain
43	chr3:119809800-119815000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:119809800-119815000	Active TSS	Fetal Intestine Small	intestine
45	chr3:119809800-119815800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:119809800-119815800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:119810000-119814600	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:119810000-119814800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:119810000-119814800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:119810000-119814800	Active TSS	Cortex derived primary cultured neurospheres	brain

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