Variant report

Variant	rs10939652
Chromosome Location	chr4:16198378-16198379
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	CTCF	chr4:16198101-16198484	GM12878	blood:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
2	RAD21	chr4:16198114-16198498	H1-hESC	embryonic stem cell:	n/a	chr4:16198433-16198442
3	CTCF	chr4:16198072-16198514	MCF-7	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
4	JUND	chr4:16198015-16198524	T-47D	breast:	n/a	n/a
5	CTCF	chr4:16198218-16198382	ProgFib	skin:	n/a	n/a
6	ZNF143	chr4:16198174-16198467	GM12878	blood:	n/a	n/a
7	SMC3	chr4:16198206-16198435	HepG2	liver:	n/a	n/a
8	CTCF	chr4:16198193-16198391	A549	lung:	n/a	n/a
9	CTCF	chr4:16198137-16198425	T-47D	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
10	CTCF	chr4:16198280-16198430	HCM	heart:	n/a	n/a
11	RAD21	chr4:16198112-16198549	A549	lung:	n/a	chr4:16198433-16198442
12	CTCF	chr4:16198174-16198386	HepG2	liver:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
13	CTCF	chr4:16198103-16198422	Kidney_OC	kidney:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
14	FOXA1	chr4:16198007-16198425	ECC-1	luminal epithelium:	n/a	n/a
15	SPI1	chr4:16198183-16198437	GM12878	blood:	n/a	n/a
16	RUNX3	chr4:16198029-16198500	GM12878	blood:	n/a	n/a
17	FOXA1	chr4:16198001-16198463	T-47D	breast:	n/a	n/a
18	CTCF	chr4:16198101-16198464	ECC-1	luminal epithelium:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
19	EP300	chr4:16197977-16198518	T-47D	breast:	n/a	chr4:16198211-16198221 chr4:16198357-16198371 chr4:16198507-16198516 chr4:16198361-16198375
20	POLR2A	chr4:16198249-16198626	MCF10A-Er-Src	breast:	n/a	n/a
21	SPI1	chr4:16198184-16198494	GM12878	blood:	n/a	n/a
22	SPI1	chr4:16197886-16198631	GM12878	blood:	n/a	chr4:16198505-16198518
23	CTCF	chr4:16198054-16198490	T-47D	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
24	SMC3	chr4:16198220-16198429	GM12878	blood:	n/a	n/a
25	CTCF	chr4:16197997-16198580	MCF-7	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
26	CTCF	chr4:16197961-16198728	HCT-116	colon:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
27	TEAD4	chr4:16198031-16198594	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr4:16198029-16198634	HCT-116	colon:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
29	CTCF	chr4:16198203-16198411	Pancreas_OC	pancreas:	n/a	n/a
30	CTCF	chr4:16198114-16198471	A549	lung:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
31	CTCF	chr4:16198120-16198390	HFF-Myc	foreskin:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
32	RAD21	chr4:16198058-16198524	H1-hESC	embryonic stem cell:	n/a	chr4:16198433-16198442
33	CTCF	chr4:16198260-16198410	A549	lung:	n/a	n/a
34	CTCF	chr4:16198170-16198485	ECC-1	luminal epithelium:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
35	CTCF	chr4:16198240-16198390	AG04450	lung:	n/a	n/a
36	CTCF	chr4:16198260-16198410	GM12878	blood:	n/a	n/a
37	STAT3	chr4:16198232-16198435	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr4:16198151-16198512	Spleen_OC	spleen:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
39	CTCF	chr4:16198300-16198450	NHLF	lung:	n/a	n/a
40	SIN3A	chr4:16198142-16198426	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr4:16198188-16198424	MCF-7	breast:	n/a	n/a
42	PRDM1	chr4:16198098-16198433	Hela-S3	cervix:	n/a	chr4:16198318-16198333
43	JUND	chr4:16198172-16198457	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr4:16198104-16198466	IMR90	lung:	n/a	chr4:16198433-16198442
45	MYC	chr4:16198179-16198556	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr4:16198240-16198390	Caco-2	colon:	n/a	n/a
47	FOXA2	chr4:16198120-16198459	A549	lung:	n/a	n/a
48	CTCF	chr4:16198240-16198390	HEK293	kidney:	n/a	n/a
49	CTCF	chr4:16198247-16198405	NHEK	skin:	n/a	n/a
50	RAD21	chr4:16198019-16198499	HCT-116	colon:	n/a	chr4:16198433-16198442

Variant related genes	Relation type
TAPT1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10019399	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516299	0.89[ASN][1000 genomes]
rs10939651	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10939653	0.85[ASN][1000 genomes]
rs12506249	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12646600	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13133263	0.81[AFR][1000 genomes]
rs1373112	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1619904	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1662650	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662654	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1662656	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178450	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044195	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28453363	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28618674	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28645901	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs317854	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs317855	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs317869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs317870	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs317871	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs317872	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs317873	0.81[AFR][1000 genomes]
rs317874	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs317875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs317876	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs317877	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs317878	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36012247	0.81[AFR][1000 genomes]
rs4395495	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7657191	0.82[ASN][1000 genomes]
rs7666361	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
6	chr4:16184200-16200600	Strong transcription	Fetal Thymus	thymus
7	chr4:16187400-16199600	Weak transcription	Hela-S3	cervix
8	chr4:16191400-16207000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:16192200-16204800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:16193000-16198400	Weak transcription	Psoas Muscle	Psoas
11	chr4:16193000-16205000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:16193000-16207600	Weak transcription	Brain Germinal Matrix	brain
13	chr4:16193000-16208200	Weak transcription	Esophagus	oesophagus
14	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
15	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
16	chr4:16193200-16198400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:16193200-16198400	Weak transcription	Fetal Stomach	stomach
18	chr4:16193200-16205800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:16193200-16206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:16193200-16207000	Weak transcription	Pancreas	Pancrea
21	chr4:16193200-16208000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:16193200-16208000	Weak transcription	Lung	lung
23	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
24	chr4:16193400-16211200	Weak transcription	Placenta	Placenta
25	chr4:16193600-16203000	Weak transcription	HepG2	liver
26	chr4:16193600-16208600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:16193800-16198800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:16193800-16206400	Weak transcription	K562	blood
29	chr4:16194200-16202400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:16195000-16204800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:16195400-16198400	Weak transcription	Aorta	Aorta
32	chr4:16195400-16199600	Weak transcription	Right Ventricle	heart
33	chr4:16195400-16199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:16195400-16199600	Weak transcription	Small Intestine	intestine
35	chr4:16195400-16201400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:16195400-16201400	Weak transcription	Left Ventricle	heart
37	chr4:16195400-16201600	Weak transcription	Thymus	Thymus
38	chr4:16195400-16203200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:16195400-16207000	Weak transcription	Gastric	stomach
40	chr4:16196000-16198400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:16196200-16198600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:16196200-16201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:16196200-16203400	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:16196200-16207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:16196600-16198600	Enhancers	Fetal Heart	heart
46	chr4:16197000-16199000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr4:16197200-16199200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr4:16197400-16198800	Strong transcription	Dnd41	blood
49	chr4:16197400-16200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:16197600-16199200	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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