Variant report

Variant	rs890871
Chromosome Location	chr19:55672055-55672056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:379)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:379 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr19:55671911-55672283	NB4	blood:	n/a	n/a
2	CTCF	chr19:55671935-55672199	HepG2	liver:	n/a	n/a
3	CTCF	chr19:55671940-55672210	HCM	heart:	n/a	n/a
4	YY1	chr19:55671948-55672256	HCT-116	colon:	n/a	chr19:55672173-55672192
5	CTCF	chr19:55672040-55672190	GM12870	blood:	n/a	n/a
6	RAD21	chr19:55671890-55672201	GM12878	blood:	n/a	chr19:55671960-55671969
7	CTCF	chr19:55672000-55672150	HFF-Myc	foreskin:	n/a	n/a
8	ATF3	chr19:55671858-55672277	K562	blood:	n/a	chr19:55672187-55672196
9	CTCF	chr19:55671980-55672130	HAc	cerebellar:	n/a	n/a
10	CTCF	chr19:55671848-55672295	A549	lung:	n/a	n/a
11	JUND	chr19:55671964-55672162	HepG2	liver:	n/a	n/a
12	CTCF	chr19:55672000-55672150	K562	blood:	n/a	n/a
13	CTCF	chr19:55672000-55672150	HPF	lung:	n/a	n/a
14	MAX	chr19:55671894-55672869	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr19:55672020-55672170	GM12878	blood:	n/a	n/a
16	USF1	chr19:55671917-55672332	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr19:55672020-55672170	GM12866	blood:	n/a	n/a
18	USF2	chr19:55671946-55672202	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr19:55671765-55672331	H1-hESC	embryonic stem cell:	n/a	chr19:55671960-55671969
20	CREB1	chr19:55671863-55672317	A549	lung:	n/a	n/a
21	CTCF	chr19:55672000-55672150	SAEC	small airway:	n/a	n/a
22	USF1	chr19:55671840-55672227	A549	lung:	n/a	n/a
23	TAF1	chr19:55671887-55672168	K562	blood:	n/a	n/a
24	CTCF	chr19:55671968-55672233	Pancreas_OC	pancreas:	n/a	n/a
25	YY1	chr19:55671926-55672315	GM12878	blood:	n/a	chr19:55672173-55672192
26	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
27	CTCF	chr19:55671815-55672241	HepG2	liver:	n/a	n/a
28	RAD21	chr19:55671693-55672448	SK-N-SH	brain:	n/a	chr19:55671960-55671969
29	E2F6	chr19:55671935-55672173	K562	blood:	n/a	n/a
30	RAD21	chr19:55671827-55672374	A549	lung:	n/a	chr19:55671960-55671969
31	CTCF	chr19:55672000-55672150	AG09319	gingival:	n/a	n/a
32	CTCF	chr19:55671970-55672220	GM13976	blood:	n/a	n/a
33	CTCF	chr19:55671911-55672313	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr19:55671890-55672304	A549	lung:	n/a	chr19:55672186-55672195
35	ZNF143	chr19:55671897-55672281	H1-hESC	embryonic stem cell:	n/a	chr19:55672196-55672215
36	SMC3	chr19:55671888-55672276	GM12878	blood:	n/a	n/a
37	BHLHE40	chr19:55671904-55672241	GM12878	blood:	n/a	n/a
38	MAX	chr19:55671877-55672254	NB4	blood:	n/a	n/a
39	BRCA1	chr19:55671889-55672277	Hela-S3	cervix:	n/a	n/a
40	MYC	chr19:55671912-55672273	MCF-7	breast:	n/a	n/a
41	ELF1	chr19:55671969-55672318	K562	blood:	n/a	n/a
42	RFX5	chr19:55672045-55672196	GM12878	blood:	n/a	n/a
43	ELF1	chr19:55671984-55672230	K562	blood:	n/a	n/a
44	BHLHE40	chr19:55671851-55672266	K562	blood:	n/a	n/a
45	USF1	chr19:55671897-55672289	K562	blood:	n/a	n/a
46	MAX	chr19:55671874-55672265	K562	blood:	n/a	n/a
47	ZMIZ1	chr19:55671652-55672249	K562	blood:	n/a	n/a
48	PBX3	chr19:55671893-55672346	SK-N-SH	brain:	n/a	n/a
49	MXI1	chr19:55671445-55672353	SK-N-SH	brain:	n/a	n/a
50	TEAD4	chr19:55671660-55672300	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55672036-55672086	NT2-D1	testis:	n/a
2	chr19:55672036-55672086	HEEpiC	esophagus:	n/a
3	chr19:55672036-55672086	BJ	skin:	n/a
4	chr19:55672036-55672086	PANC-1	pancreas:	n/a
5	chr19:55672036-55672086	HUVEC	blood vessel:	n/a
6	chr19:55672036-55672086	MCF10A-Er-Src	breast:	n/a
7	chr19:55672036-55672086	GM12878	blood:	n/a
8	chr19:55672036-55672086	HRPEpiC	eye:	n/a
9	chr19:55672036-55672086	LNCaP	prostate:	n/a
10	chr19:55672036-55672086	HCT-116	colon:	n/a
11	chr19:55672036-55672086	HRCEpiC	kidney:	n/a
12	chr19:55672036-55672086	Hepatocyte	liver:	n/a
13	chr19:55672036-55672086	HPAEpiC	pulmonary alveolar:	n/a
14	chr19:55672036-55672086	HCF	heart:	n/a
15	chr19:55672036-55672086	HRE	kidney:	n/a
16	chr19:55672036-55672086	HL-60	blood:	n/a
17	chr19:55672036-55672086	U87	brain:	n/a
18	chr19:55672036-55672086	HAEpiC	amniotic membrane:	n/a
19	chr19:55672036-55672086	Caco-2	colon:	n/a
20	chr19:55672036-55672086	SKMC	muscle:	n/a
21	chr19:55672036-55672086	HIPEpiC	eye:	n/a
22	chr19:55672036-55672086	SK-N-MC	brain:	n/a
23	chr19:55672036-55672086	ECC-1	luminal epithelium:	n/a
24	chr19:55672036-55672086	ProgFib	skin:	n/a
25	chr19:55672036-55672086	HEK293	kidney:	embryo
26	chr19:55672036-55672086	HCM	heart:	n/a
27	chr19:55672036-55672086	Hela-S3	cervix:	n/a
28	chr19:55672036-55672086	BE2_C	brain:	n/a
29	chr19:55672036-55672086	PrEC	prostate:	n/a
30	chr19:55672036-55672086	SK-N-SH_RA	brain:	n/a
31	chr19:55672036-55672086	NHDF-neo	bronchial:	n/a
32	chr19:55672036-55672086	AG09319	gingival:	n/a
33	chr19:55672036-55672086	PFSK-1	brain:	n/a
34	chr19:55672036-55672086	RPTEC	kidney:	n/a
35	chr19:55672036-55672086	HNPCEpiC	eye:	n/a
36	chr19:55672036-55672086	AG09309	skin:	n/a
37	chr19:55672036-55672086	IMR90	lung:	fetal
38	chr19:55672036-55672086	K562	blood:	n/a
39	chr19:55672036-55672086	GM12892	blood:	n/a
40	chr19:55672036-55672086	Jurkat	blood:	n/a
41	chr19:55672036-55672086	HepG2	liver:	n/a
42	chr19:55672036-55672086	AG10803	skin:	n/a
43	chr19:55672036-55672086	AoSMC	blood vessel:	n/a
44	chr19:55672036-55672086	GM12891	blood:	n/a
45	chr19:55672036-55672086	H1-hESC	embryonic stem cell:	embryo
46	chr19:55672036-55672086	MCF-7	breast:	n/a
47	chr19:55672036-55672086	AG04449	skin:	fetal
48	chr19:55672036-55672086	T-47D	breast:	n/a
49	chr19:55672036-55672086	GM06990	blood:	n/a
50	chr19:55672036-55672086	NHBE	bronchial:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55670339..55672194-chr19:55895106..55898791,3	K562	blood:
2	chr19:55650102..55652468-chr19:55670117..55672433,2	K562	blood:
3	chr19:55579852..55582710-chr19:55671936..55674879,2	K562	blood:
4	chr19:55656068..55658188-chr19:55669727..55672257,4	K562	blood:
5	chr19:55657215..55657931-chr19:55671632..55672517,3	K562	blood:
6	chr19:55669904..55673815-chr19:55917688..55921815,5	K562	blood:
7	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
8	chr19:55657176..55657861-chr19:55671612..55672279,3	MCF-7	breast:
9	chr19:55670803..55672973-chr19:55678461..55680015,2	MCF-7	breast:
10	chr19:55669094..55672573-chr19:55676633..55678240,3	K562	blood:
11	chr19:55590282..55593983-chr19:55668450..55672239,5	K562	blood:
12	chr19:55652274..55653243-chr19:55671651..55672648,4	K562	blood:
13	chr19:55657720..55659447-chr19:55670409..55672561,2	MCF-7	breast:
14	chr19:55670813..55674787-chr19:55917654..55919984,3	MCF-7	breast:
15	chr19:55656783..55658511-chr19:55670096..55672623,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000267110	TF binding region
TNNI3	TF binding region
DNAAF3	TF binding region
ENSG00000267110	CpG island
TNNI3	CpG island
DNAAF3	CpG island
ENSG00000108107	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000131037	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10421953	0.85[ASN][1000 genomes]
rs10423713	0.86[ASN][1000 genomes]
rs1128712	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12459688	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12459887	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12459917	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12459921	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12459930	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460445	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12461148	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12461170	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12461195	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461202	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462211	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17458	0.86[AMR][1000 genomes]
rs2071572	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071574	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278281	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288420	0.86[AMR][1000 genomes]
rs2288528	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2301278	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3745922	0.86[AMR][1000 genomes]
rs3786867	0.94[ASN][1000 genomes]
rs3826887	0.90[AMR][1000 genomes]
rs3848618	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3859544	0.92[ASN][1000 genomes]
rs56666700	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56726774	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58017412	0.86[AMR][1000 genomes]
rs58218194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58824375	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59663064	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60176657	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60799292	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61570139	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7255625	0.95[ASN][1000 genomes]
rs9710458	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][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	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	esv3375469	chr19:55671705-55672069	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	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:43 , 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	chr19:55669200-55672200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:55669200-55672800	Enhancers	Fetal Heart	heart
4	chr19:55669600-55672400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr19:55669600-55673400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr19:55669800-55672400	Enhancers	A549	lung
7	chr19:55670000-55672200	Flanking Active TSS	Hela-S3	cervix
8	chr19:55670000-55672400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:55670400-55672200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr19:55670400-55672400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:55670400-55672400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr19:55670600-55672200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:55670600-55672200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:55670800-55673800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
15	chr19:55671000-55673000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:55671400-55672600	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr19:55671600-55672200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr19:55671600-55672200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:55671600-55672200	Bivalent Enhancer	Fetal Thymus	thymus
20	chr19:55671600-55672200	Enhancers	Right Ventricle	heart
21	chr19:55671600-55672400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:55671600-55672600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
23	chr19:55671600-55672800	Bivalent Enhancer	Placenta	Placenta
24	chr19:55671600-55677600	Weak transcription	Right Atrium	heart
25	chr19:55671800-55672400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:55671800-55672600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:55671800-55677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:55672000-55672200	Enhancers	Spleen	Spleen
29	chr19:55672000-55672200	Active TSS	K562	blood
30	chr19:55672000-55672400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:55672000-55672400	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:55672000-55672400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:55672000-55672400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:55672000-55672400	Weak transcription	Left Ventricle	heart
35	chr19:55672000-55672600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr19:55672000-55672600	Enhancers	Pancreas	Pancrea
37	chr19:55672000-55672800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:55672000-55672800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr19:55672000-55672800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:55672000-55673000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr19:55672000-55673400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr19:55672000-55673400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
43	chr19:55672000-55677200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links