Variant report

Variant	rs59663064
Chromosome Location	chr19:55672298-55672299
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	MAX	chr19:55671894-55672869	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr19:55671917-55672332	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr19:55671765-55672331	H1-hESC	embryonic stem cell:	n/a	chr19:55671960-55671969
4	CREB1	chr19:55671863-55672317	A549	lung:	n/a	n/a
5	YY1	chr19:55671926-55672315	GM12878	blood:	n/a	chr19:55672173-55672192
6	SP1	chr19:55671925-55672377	H1-hESC	embryonic stem cell:	n/a	chr19:55672155-55672165 chr19:55672154-55672166 chr19:55672260-55672272 chr19:55672188-55672197 chr19:55672186-55672198 chr19:55672187-55672196 chr19:55672186-55672198 chr19:55672154-55672166 chr19:55672186-55672197 chr19:55672262-55672271 chr19:55672155-55672165 chr19:55672188-55672197
7	RAD21	chr19:55671693-55672448	SK-N-SH	brain:	n/a	chr19:55671960-55671969
8	RAD21	chr19:55671827-55672374	A549	lung:	n/a	chr19:55671960-55671969
9	CTCF	chr19:55671911-55672313	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr19:55671890-55672304	A549	lung:	n/a	chr19:55672186-55672195
11	ELF1	chr19:55671969-55672318	K562	blood:	n/a	n/a
12	PBX3	chr19:55671893-55672346	SK-N-SH	brain:	n/a	n/a
13	MXI1	chr19:55671445-55672353	SK-N-SH	brain:	n/a	n/a
14	TEAD4	chr19:55671660-55672300	K562	blood:	n/a	n/a
15	MAX	chr19:55671691-55672443	A549	lung:	n/a	n/a
16	CREB1	chr19:55671898-55672639	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr19:55671669-55672417	HCT-116	colon:	n/a	n/a
18	E2F4	chr19:55671952-55672344	MCF10A-Er-Src	breast:	n/a	n/a
19	SP4	chr19:55671842-55672609	H1-hESC	embryonic stem cell:	n/a	chr19:55672150-55672166 chr19:55672152-55672168 chr19:55672184-55672200 chr19:55672186-55672197
20	MAX	chr19:55671844-55672324	MCF-7	breast:	n/a	n/a
21	YY1	chr19:55671878-55672328	HepG2	liver:	n/a	chr19:55672173-55672192
22	MYC	chr19:55671465-55672301	K562	blood:	n/a	n/a
23	MAX	chr19:55671877-55672322	SK-N-SH	brain:	n/a	n/a
24	USF1	chr19:55671891-55672336	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr19:55671359-55672503	HCT-116	colon:	n/a	n/a
26	HCFC1	chr19:55671601-55672360	Hela-S3	cervix:	n/a	n/a
27	E2F6	chr19:55671853-55672895	H1-hESC	embryonic stem cell:	n/a	chr19:55672795-55672807
28	MAZ	chr19:55671895-55672301	GM12878	blood:	n/a	n/a
29	GTF2F1	chr19:55671906-55672304	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr19:55671792-55672762	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr19:55671872-55672331	ECC-1	luminal epithelium:	n/a	chr19:55671960-55671969
32	IRF1	chr19:55671934-55672420	K562	blood:	n/a	chr19:55672260-55672274 chr19:55672154-55672168 chr19:55672186-55672200
33	POLR2A	chr19:55672282-55672488	H1-hESC	embryonic stem cell:	n/a	n/a
34	SMC3	chr19:55671712-55672321	Hela-S3	cervix:	n/a	n/a
35	HDAC2	chr19:55671885-55672313	K562	blood:	n/a	n/a
36	MAZ	chr19:55671798-55672441	K562	blood:	n/a	n/a
37	PML	chr19:55671881-55672322	GM12878	blood:	n/a	n/a
38	JUND	chr19:55671944-55672303	H1-hESC	embryonic stem cell:	n/a	chr19:55672186-55672195
39	FOSL2	chr19:55671733-55672332	A549	lung:	n/a	chr19:55672186-55672195
40	MAX	chr19:55671378-55672353	HCT-116	colon:	n/a	n/a
41	TBP	chr19:55671876-55672553	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr19:55671426-55672696	A549	lung:	n/a	n/a
43	MAX	chr19:55671823-55672378	ECC-1	luminal epithelium:	n/a	n/a
44	RAD21	chr19:55671663-55672478	HCT-116	colon:	n/a	chr19:55671960-55671969
45	JUN	chr19:55669767-55672364	K562	blood:	n/a	chr19:55672186-55672195
46	HMGN3	chr19:55671922-55672576	K562	blood:	n/a	n/a
47	RAD21	chr19:55671847-55672306	SK-N-SH_RA	brain:	n/a	chr19:55671960-55671969
48	CBX3	chr19:55671767-55672356	K562	blood:	n/a	n/a
49	TCF12	chr19:55671755-55672457	A549	lung:	n/a	chr19:55671958-55671965
50	FOXP2	chr19:55671915-55672687	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55650102..55652468-chr19:55670117..55672433,2	K562	blood:
2	chr19:55627388..55629698-chr19:55672061..55673602,2	K562	blood:
3	chr19:55579852..55582710-chr19:55671936..55674879,2	K562	blood:
4	chr19:55657215..55657931-chr19:55671632..55672517,3	K562	blood:
5	chr19:55669904..55673815-chr19:55917688..55921815,5	K562	blood:
6	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
7	chr19:55670803..55672973-chr19:55678461..55680015,2	MCF-7	breast:
8	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
9	chr19:55669094..55672573-chr19:55676633..55678240,3	K562	blood:
10	chr19:55652274..55653243-chr19:55671651..55672648,4	K562	blood:
11	chr19:55657720..55659447-chr19:55670409..55672561,2	MCF-7	breast:
12	chr19:55670813..55674787-chr19:55917654..55919984,3	MCF-7	breast:
13	chr19:55656783..55658511-chr19:55670096..55672623,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55671860-55672582	NONHSAT067998
2	lnc-EPS8L1-2	chr19:55671860-55672582	NONHSAT067999

Variant related genes	Relation type
DNAAF3	TF binding region
ENSG00000267110	TF binding region
TNNI3	TF binding region
ENSG00000125503	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000160439	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10421953	0.86[ASN][1000 genomes]
rs10423713	0.87[ASN][1000 genomes]
rs1128712	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12459688	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459887	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459917	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459921	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12459930	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12460445	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12461148	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12461170	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12461195	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12461202	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462211	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17458	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2071572	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2071574	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278281	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288420	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2288528	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288529	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2301278	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3745922	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3786867	0.95[ASN][1000 genomes]
rs3826887	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3848618	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859544	0.93[ASN][1000 genomes]
rs56666700	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56726774	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58017412	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58218194	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58824375	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60176657	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60799292	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61570139	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255625	0.96[ASN][1000 genomes]
rs890871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9710458	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[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	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55669000-55672800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
2	chr19:55669200-55672800	Enhancers	Fetal Heart	heart
3	chr19:55669600-55672400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr19:55669600-55673400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr19:55669800-55672400	Enhancers	A549	lung
6	chr19:55670000-55672400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:55670400-55672400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:55670400-55672400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr19:55670800-55673800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr19:55671000-55673000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:55671400-55672600	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr19:55671600-55672400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:55671600-55672600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
14	chr19:55671600-55672800	Bivalent Enhancer	Placenta	Placenta
15	chr19:55671600-55677600	Weak transcription	Right Atrium	heart
16	chr19:55671800-55672400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:55671800-55672600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:55671800-55677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:55672000-55672400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:55672000-55672400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:55672000-55672400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:55672000-55672400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:55672000-55672400	Weak transcription	Left Ventricle	heart
24	chr19:55672000-55672600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr19:55672000-55672600	Enhancers	Pancreas	Pancrea
26	chr19:55672000-55672800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr19:55672000-55672800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr19:55672000-55672800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:55672000-55673000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr19:55672000-55673400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:55672000-55673400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr19:55672000-55677200	Weak transcription	NHEK	skin
33	chr19:55672200-55672400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr19:55672200-55672400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:55672200-55672400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:55672200-55672400	Weak transcription	Spleen	Spleen
37	chr19:55672200-55672600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:55672200-55672600	Flanking Active TSS	Right Ventricle	heart
39	chr19:55672200-55672600	Weak transcription	K562	blood
40	chr19:55672200-55673600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:55672200-55676800	Weak transcription	Hela-S3	cervix

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