Variant report

Variant	rs72938238
Chromosome Location	chr3:111578286-111578287
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	EGR1	chr3:111578220-111578683	H1-hESC	embryonic stem cell:	n/a	chr3:111578428-111578438 chr3:111578546-111578559 chr3:111578650-111578660 chr3:111578449-111578464
2	CHD2	chr3:111577489-111579719	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:111577360-111579652	HCT-116	colon:	n/a	n/a
4	POLR2A	chr3:111577188-111584197	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:111578112-111578384	HepG2	liver:	n/a	n/a
6	RAD21	chr3:111577736-111578305	A549	lung:	n/a	n/a
7	POLR2A	chr3:111578053-111578533	A549	lung:	n/a	n/a
8	HEY1	chr3:111578014-111578475	HepG2	liver:	n/a	n/a
9	MAZ	chr3:111577919-111579365	HepG2	liver:	n/a	chr3:111578651-111578661
10	POLR2A	chr3:111577985-111579708	U87	brain:	n/a	n/a
11	POLR2A	chr3:111577950-111579334	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:111578092-111578829	ECC-1	luminal epithelium:	n/a	n/a
13	E2F1	chr3:111577579-111578872	Hela-S3	cervix:	n/a	chr3:111578683-111578693
14	POLR2A	chr3:111578093-111579437	Gliobla	brain:	n/a	n/a
15	USF2	chr3:111577507-111578355	Hela-S3	cervix:	n/a	chr3:111577993-111578004
16	POLR2A	chr3:111577901-111580077	HUVEC	blood vessel:	n/a	n/a
17	MAFK	chr3:111577500-111579854	Hela-S3	cervix:	n/a	n/a
18	TBP	chr3:111577495-111578291	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr3:111577868-111578336	H1-hESC	embryonic stem cell:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
20	MYC	chr3:111577418-111578670	MCF10A-Er-Src	breast:	n/a	chr3:111578651-111578661
21	POLR2A	chr3:111577494-111580766	Hela-S3	cervix:	n/a	n/a
22	SIN3AK20	chr3:111577497-111579715	HCT-116	colon:	n/a	n/a
23	EP300	chr3:111577782-111579719	SK-N-SH	brain:	n/a	chr3:111578477-111578490 chr3:111578300-111578316 chr3:111578900-111578913 chr3:111577922-111577936 chr3:111578681-111578690
24	SMARCB1	chr3:111577559-111579652	Hela-S3	cervix:	n/a	n/a
25	CHD1	chr3:111578166-111579462	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZBTB7A	chr3:111578281-111578701	HepG2	liver:	n/a	chr3:111578344-111578352 chr3:111578434-111578445 chr3:111578435-111578446
27	JUND	chr3:111577867-111578815	A549	lung:	n/a	chr3:111578782-111578796
28	POLR2A	chr3:111578061-111578749	A549	lung:	n/a	n/a
29	CEBPB	chr3:111577822-111578569	HepG2	liver:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
30	TAF1	chr3:111577883-111579607	SK-N-SH	brain:	n/a	n/a
31	FOXA1	chr3:111577830-111578423	HepG2	liver:	n/a	n/a
32	MYBL2	chr3:111577902-111578454	HepG2	liver:	n/a	n/a
33	HA-E2F1	chr3:111577774-111579780	MCF-7	breast:	n/a	chr3:111578683-111578693 chr3:111579168-111579175 chr3:111579580-111579590
34	CEBPB	chr3:111577674-111578352	MCF-7	breast:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
35	TBP	chr3:111578190-111578732	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:111578074-111578382	HepG2	liver:	n/a	n/a
37	KAT2A	chr3:111577942-111578452	Hela-S3	cervix:	n/a	n/a
38	JUND	chr3:111578205-111578632	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:111577991-111579657	U87	brain:	n/a	n/a
40	TAF1	chr3:111578070-111579046	H1-hESC	embryonic stem cell:	n/a	n/a
41	ZBTB7A	chr3:111578051-111579227	ECC-1	luminal epithelium:	n/a	chr3:111578344-111578352 chr3:111578434-111578445 chr3:111578435-111578446
42	POLR2A	chr3:111577868-111578386	HepG2	liver:	n/a	n/a
43	TFAP2A	chr3:111577378-111578577	Hela-S3	cervix:	n/a	chr3:111577962-111577977 chr3:111577963-111577974 chr3:111577965-111577973 chr3:111577964-111577972 chr3:111578326-111578334 chr3:111577963-111577974 chr3:111577964-111577972 chr3:111577963-111577974 chr3:111577965-111577973 chr3:111577965-111577973 chr3:111577963-111577974 chr3:111577964-111577972
44	POLR2A	chr3:111577424-111580051	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:111578016-111578947	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr3:111577624-111580773	HUVEC	blood vessel:	n/a	n/a
47	SIX5	chr3:111578227-111578575	H1-hESC	embryonic stem cell:	n/a	n/a
48	CEBPB	chr3:111577401-111578727	Hela-S3	cervix:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
49	MXI1	chr3:111577557-111578739	HepG2	liver:	n/a	n/a
50	SP4	chr3:111578103-111578478	H1-hESC	embryonic stem cell:	n/a	chr3:111578450-111578466

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:111578238-111578288	PFSK-1	brain:	n/a
2	chr3:111578238-111578288	SK-N-SH_RA	brain:	n/a
3	chr3:111578238-111578288	HEK293	kidney:	embryo
4	chr3:111578238-111578288	HCT-116	colon:	n/a
5	chr3:111578238-111578288	HRCEpiC	kidney:	n/a
6	chr3:111578238-111578288	AG04449	skin:	fetal
7	chr3:111578238-111578288	LNCaP	prostate:	n/a
8	chr3:111578238-111578288	NHBE	bronchial:	n/a
9	chr3:111578238-111578288	GM12892	blood:	n/a
10	chr3:111578238-111578288	ECC-1	luminal epithelium:	n/a
11	chr3:111578238-111578288	T-47D	breast:	n/a
12	chr3:111578238-111578288	PrEC	prostate:	n/a
13	chr3:111578238-111578288	PANC-1	pancreas:	n/a
14	chr3:111578238-111578288	HPAEpiC	pulmonary alveolar:	n/a
15	chr3:111578238-111578288	AG04450	lung:	fetal
16	chr3:111578238-111578288	HEEpiC	esophagus:	n/a
17	chr3:111578238-111578288	NT2-D1	testis:	n/a
18	chr3:111578238-111578288	HL-60	blood:	n/a
19	chr3:111578238-111578288	HMEC	breast:	n/a
20	chr3:111578238-111578288	HIPEpiC	eye:	n/a
21	chr3:111578238-111578288	HRE	kidney:	n/a
22	chr3:111578238-111578288	HepG2	liver:	n/a
23	chr3:111578238-111578288	GM06990	blood:	n/a
24	chr3:111578238-111578288	HCF	heart:	n/a
25	chr3:111578238-111578288	H1-hESC	embryonic stem cell:	embryo
26	chr3:111578238-111578288	AG09309	skin:	n/a
27	chr3:111578238-111578288	GM12891	blood:	n/a
28	chr3:111578238-111578288	AG10803	skin:	n/a
29	chr3:111578238-111578288	SKMC	muscle:	n/a
30	chr3:111578238-111578288	SAEC	small airway:	n/a
31	chr3:111578238-111578288	HUVEC	blood vessel:	n/a
32	chr3:111578238-111578288	RPTEC	kidney:	n/a
33	chr3:111578238-111578288	MCF10A-Er-Src	breast:	n/a
34	chr3:111578238-111578288	HRPEpiC	eye:	n/a
35	chr3:111578238-111578288	ProgFib	skin:	n/a
36	chr3:111578238-111578288	MCF-7	breast:	n/a
37	chr3:111578238-111578288	Jurkat	blood:	n/a
38	chr3:111578238-111578288	NH-A	brain:	n/a
39	chr3:111578238-111578288	Hela-S3	cervix:	n/a
40	chr3:111578238-111578288	U87	brain:	n/a
41	chr3:111578238-111578288	AG09319	gingival:	n/a
42	chr3:111578238-111578288	HCPEpiC	choroid plexus:	n/a
43	chr3:111578238-111578288	IMR90	lung:	fetal
44	chr3:111578238-111578288	Hepatocyte	liver:	n/a
45	chr3:111578238-111578288	BE2_C	brain:	n/a
46	chr3:111578238-111578288	Caco-2	colon:	n/a
47	chr3:111578238-111578288	CMK	blood:	n/a
48	chr3:111578238-111578288	GM12878	blood:	n/a
49	chr3:111578238-111578288	K562	blood:	n/a
50	chr3:111578238-111578288	SK-N-MC	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:26231550..26232395-chr3:111577908..111578543,2	Hela-S3	cervix:
2	chr16:9185258..9185924-chr3:111577985..111578506,2	Hela-S3	cervix:
3	chr1:167906032..167906543-chr3:111577920..111578725,2	Hela-S3	cervix:
4	chr3:111576494..111579081-chr3:111696421..111699159,2	MCF-7	breast:

Variant related genes	Relation type
PHLDB2	TF binding region
PHLDB2	CpG island
ENSG00000144827	Chromatin interaction
ENSG00000143164	Chromatin interaction
ENSG00000182831	Chromatin interaction
ENSG00000143158	Chromatin interaction
ENSG00000117632	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1282974	0.83[AMR][1000 genomes]
rs57784706	1.00[AMR][1000 genomes]
rs72936491	0.83[AMR][1000 genomes]
rs72938226	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72938229	0.83[AMR][1000 genomes]
rs72938231	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72938235	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72938239	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938244	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111577400-111579200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
2	chr3:111577400-111580200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:111577400-111581000	Active TSS	Right Ventricle	heart
4	chr3:111577400-111581200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:111577400-111582000	Active TSS	Aorta	Aorta
6	chr3:111577400-111582000	Active TSS	HSMMtube	muscle
7	chr3:111577600-111578400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:111577600-111578400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
9	chr3:111577600-111578600	Flanking Active TSS	Liver	Liver
10	chr3:111577600-111578800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
11	chr3:111577600-111579400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
12	chr3:111577600-111579600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:111577600-111579600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:111577600-111579600	Active TSS	Duodenum Mucosa	Duodenum
15	chr3:111577600-111580200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:111577600-111580200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
17	chr3:111577600-111580200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr3:111577600-111580400	Active TSS	Fetal Heart	heart
19	chr3:111577600-111581200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:111577600-111581800	Active TSS	Left Ventricle	heart
21	chr3:111577800-111578400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr3:111577800-111578400	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr3:111577800-111578400	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr3:111577800-111578400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr3:111577800-111578400	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr3:111577800-111578400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr3:111577800-111578400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:111577800-111578400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:111577800-111578400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr3:111577800-111578400	Bivalent Enhancer	Fetal Brain Male	brain
31	chr3:111577800-111578400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:111577800-111578400	Bivalent/Poised TSS	Thymus	Thymus
33	chr3:111577800-111578600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
34	chr3:111577800-111579000	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:111577800-111579000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:111577800-111579000	Bivalent/Poised TSS	Psoas Muscle	Psoas
37	chr3:111577800-111579200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:111577800-111579600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:111577800-111579600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr3:111577800-111579600	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr3:111577800-111579600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:111577800-111579600	Active TSS	Fetal Intestine Large	intestine
43	chr3:111577800-111579800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:111577800-111579800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:111577800-111579800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:111577800-111579800	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:111577800-111579800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:111577800-111579800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:111577800-111579800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:111577800-111579800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links