Variant report

Variant	rs66707428
Chromosome Location	chr19:55628609-55628610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:61)
Chromatin interactive
region (count:40)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr19:55627332-55630427	K562	blood:	n/a	chr19:55628919-55628928 chr19:55629056-55629065 chr19:55627544-55627553 chr19:55630135-55630146
2	POLR2A	chr19:55627602-55629469	IMR90	lung:	n/a	n/a
3	CTCF	chr19:55628480-55628630	SAEC	small airway:	n/a	chr19:55628529-55628538 chr19:55628528-55628541
4	POLR2A	chr19:55628602-55628612	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr19:55628457-55628621	MCF-7	breast:	n/a	chr19:55628529-55628538 chr19:55628528-55628541
6	TAF1	chr19:55628369-55629395	HepG2	liver:	n/a	n/a
7	MXI1	chr19:55628437-55629412	HepG2	liver:	n/a	n/a
8	YY1	chr19:55628395-55630077	K562	blood:	n/a	chr19:55628918-55628932 chr19:55628888-55628908 chr19:55629065-55629076
9	YY1	chr19:55628407-55629684	HepG2	liver:	n/a	chr19:55628918-55628932 chr19:55628888-55628908 chr19:55629065-55629076
10	HCFC1	chr19:55627626-55630201	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:55627585-55629534	Raji	blood:	n/a	n/a
12	POLR2A	chr19:55627773-55629804	HepG2	liver:	n/a	n/a
13	MAX	chr19:55627313-55630331	A549	lung:	n/a	chr19:55627724-55627733 chr19:55627722-55627735 chr19:55627724-55627733
14	CTCF	chr19:55628520-55628670	GM12870	blood:	n/a	chr19:55628529-55628538 chr19:55628528-55628541
15	REST	chr19:55627570-55630206	H1-neurons	neurons:	n/a	chr19:55629066-55629079 chr19:55628004-55628024 chr19:55629991-55630005 chr19:55629046-55629060
16	E2F6	chr19:55628588-55629014	K562	blood:	n/a	n/a
17	UBTF	chr19:55628470-55628870	K562	blood:	n/a	n/a
18	POLR2A	chr19:55628502-55629486	GM18526	blood:	n/a	n/a
19	ELF1	chr19:55627602-55629522	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:55628603-55629597	GM12892	blood:	n/a	n/a
21	HA-E2F1	chr19:55628451-55629382	Hela-S3	cervix:	n/a	chr19:55629057-55629066 chr19:55629055-55629064
22	SIN3A	chr19:55628108-55630517	H1-hESC	embryonic stem cell:	n/a	chr19:55629066-55629079 chr19:55628552-55628565 chr19:55629045-55629059
23	SIN3AK20	chr19:55627836-55629503	PANC-1	pancreas:	n/a	n/a
24	ZBTB7A	chr19:55628280-55628693	ECC-1	luminal epithelium:	n/a	n/a
25	MXI1	chr19:55626740-55628692	SK-N-SH	brain:	n/a	n/a
26	CREB1	chr19:55628409-55630116	HepG2	liver:	n/a	chr19:55629054-55629067
27	POLR2A	chr19:55628580-55629586	GM12892	blood:	n/a	n/a
28	CREB1	chr19:55628325-55629515	A549	lung:	n/a	chr19:55629054-55629067
29	CTCF	chr19:55628460-55628610	SAEC	small airway:	n/a	chr19:55628529-55628538 chr19:55628528-55628541
30	MAZ	chr19:55626583-55630118	IMR90	lung:	n/a	chr19:55627724-55627733 chr19:55627722-55627735 chr19:55627724-55627733
31	POLR2A	chr19:55627605-55630390	K562	blood:	n/a	n/a
32	POLR2A	chr19:55628485-55629549	GM15510	blood:	n/a	n/a
33	HMGN3	chr19:55628386-55629297	K562	blood:	n/a	n/a
34	MYC	chr19:55628473-55628773	MCF-7	breast:	n/a	n/a
35	ATF3	chr19:55628573-55628824	K562	blood:	n/a	n/a
36	POLR2A	chr19:55628311-55629512	A549	lung:	n/a	n/a
37	E2F1	chr19:55628496-55629382	Hela-S3	cervix:	n/a	chr19:55629057-55629066 chr19:55629055-55629064
38	ELF1	chr19:55627459-55628774	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:55628551-55629393	A549	lung:	n/a	n/a
40	POLR2A	chr19:55628593-55629549	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr19:55627598-55628646	SK-N-MC	brain:	n/a	n/a
42	UBTF	chr19:55628556-55628781	K562	blood:	n/a	n/a
43	POLR2A	chr19:55628517-55629609	ProgFib	skin:	n/a	n/a
44	MXI1	chr19:55627308-55630124	IMR90	lung:	n/a	n/a
45	ZNF263	chr19:55627299-55628758	HEK293-T-REx	kidney:	n/a	chr19:55628516-55628525 chr19:55627798-55627819
46	CCNT2	chr19:55628590-55629357	K562	blood:	n/a	n/a
47	POLR2A	chr19:55627557-55629575	MCF-7	breast:	n/a	n/a
48	CREB1	chr19:55628286-55629472	K562	blood:	n/a	chr19:55629054-55629067
49	SIN3AK20	chr19:55628336-55628942	K562	blood:	n/a	n/a
50	POLR2A	chr19:55627663-55630430	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55628570-55628620	HCT-116	colon:	n/a
2	chr19:55628570-55628620	T-47D	breast:	n/a
3	chr19:55628570-55628620	IMR90	lung:	fetal
4	chr19:55628570-55628620	AG04450	lung:	fetal
5	chr19:55628570-55628620	GM12891	blood:	n/a
6	chr19:55628570-55628620	A549	lung:	n/a
7	chr19:55628570-55628620	HIPEpiC	eye:	n/a
8	chr19:55628570-55628620	PANC-1	pancreas:	n/a
9	chr19:55628570-55628620	CMK	blood:	n/a
10	chr19:55628570-55628620	HMEC	breast:	n/a
11	chr19:55628570-55628620	GM12878	blood:	n/a
12	chr19:55628570-55628620	U87	brain:	n/a
13	chr19:55628570-55628620	SKMC	muscle:	n/a
14	chr19:55628570-55628620	PrEC	prostate:	n/a
15	chr19:55628570-55628620	AG09319	gingival:	n/a
16	chr19:55628570-55628620	GM06990	blood:	n/a
17	chr19:55628570-55628620	SK-N-SH	brain:	n/a
18	chr19:55628570-55628620	K562	blood:	n/a
19	chr19:55628570-55628620	AoSMC	blood vessel:	n/a
20	chr19:55628570-55628620	Caco-2	colon:	n/a
21	chr19:55628570-55628620	SK-N-SH_RA	brain:	n/a
22	chr19:55628570-55628620	HepG2	liver:	n/a
23	chr19:55628570-55628620	HRE	kidney:	n/a
24	chr19:55628570-55628620	BE2_C	brain:	n/a
25	chr19:55628570-55628620	HEEpiC	esophagus:	n/a
26	chr19:55628570-55628620	Jurkat	blood:	n/a
27	chr19:55628570-55628620	NB4	blood:	n/a
28	chr19:55628570-55628620	HUVEC	blood vessel:	n/a
29	chr19:55628570-55628620	ProgFib	skin:	n/a
30	chr19:55628570-55628620	GM19239	blood:	n/a
31	chr19:55628570-55628620	ovcar-3	ovarian:	n/a
32	chr19:55628570-55628620	HAEpiC	amniotic membrane:	n/a
33	chr19:55628570-55628620	SAEC	small airway:	n/a
34	chr19:55628570-55628620	HCM	heart:	n/a
35	chr19:55628570-55628620	HRPEpiC	eye:	n/a
36	chr19:55628570-55628620	PFSK-1	brain:	n/a
37	chr19:55628570-55628620	GM12892	blood:	n/a
38	chr19:55628570-55628620	HPAEpiC	pulmonary alveolar:	n/a
39	chr19:55628570-55628620	HL-60	blood:	n/a
40	chr19:55628570-55628620	NHDF-neo	bronchial:	n/a
41	chr19:55628570-55628620	LNCaP	prostate:	n/a
42	chr19:55628570-55628620	NH-A	brain:	n/a
43	chr19:55628570-55628620	HCPEpiC	choroid plexus:	n/a
44	chr19:55628570-55628620	SK-N-MC	brain:	n/a
45	chr19:55628570-55628620	H1-hESC	embryonic stem cell:	embryo
46	chr19:55628570-55628620	NT2-D1	testis:	n/a
47	chr19:55628570-55628620	RPTEC	kidney:	n/a
48	chr19:55628570-55628620	AG09309	skin:	n/a
49	chr19:55628570-55628620	HEK293	kidney:	embryo
50	chr19:55628570-55628620	AG10803	skin:	n/a

(count:40 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55606533..55609893-chr19:55627288..55629671,4	MCF-7	breast:
2	chr19:55627421..55629071-chr19:56166474..56168541,2	MCF-7	breast:
3	chr19:55590301..55596157-chr19:55624719..55630906,19	K562	blood:
4	chr19:55627278..55631711-chr19:55917816..55921434,6	K562	blood:
5	chr19:55627370..55630159-chr19:56652326..56655281,2	MCF-7	breast:
6	chr19:55601384..55605740-chr19:55625589..55630501,6	MCF-7	breast:
7	chr19:55591309..55594573-chr19:55626629..55629730,4	MCF-7	breast:
8	chr19:55573131..55575554-chr19:55627229..55630312,3	K562	blood:
9	chr19:55572074..55574772-chr19:55626716..55630173,3	K562	blood:
10	chr19:55624933..55628932-chr19:55685116..55688802,5	K562	blood:
11	chr19:55628447..55630304-chr19:56152037..56154900,2	K562	blood:
12	chr19:55627804..55630494-chr19:55895380..55898353,2	K562	blood:
13	chr19:55627388..55630131-chr19:55656157..55658314,2	MCF-7	breast:
14	chr19:55627390..55629908-chr19:55969619..55972403,2	K562	blood:
15	chr19:54703373..54705649-chr19:55627800..55630510,2	K562	blood:
16	chr19:55589341..55594280-chr19:55623400..55630615,14	K562	blood:
17	chr19:55627370..55629030-chr19:55666382..55669249,2	MCF-7	breast:
18	chr19:55580586..55583113-chr19:55627733..55630223,2	MCF-7	breast:
19	chr19:55626838..55628634-chr19:56630662..56632626,2	MCF-7	breast:
20	chr19:55626998..55630422-chr19:55645937..55649783,3	K562	blood:
21	chr19:55627602..55630542-chr19:55666165..55668443,2	K562	blood:
22	chr19:55627889..55630005-chr19:55651215..55652810,2	K562	blood:
23	chr19:55627369..55630419-chr19:55655174..55659516,5	K562	blood:
24	chr19:55627599..55630640-chr19:55656141..55660358,7	K562	blood:
25	chr12:52447182..52448351-chr19:55628509..55629204,3	Hela-S3	cervix:
26	chr19:55626891..55629240-chr19:55658482..55660842,2	MCF-7	breast:
27	chr19:55628556..55629065-chr7:105162615..105163265,2	Hela-S3	cervix:
28	chr19:55627620..55630057-chr19:55971459..55973529,2	MCF-7	breast:
29	chr19:55627388..55629698-chr19:55672061..55673602,2	K562	blood:
30	chr19:55625250..55627278-chr19:55627441..55628964,2	MCF-7	breast:
31	chr19:55626440..55629266-chr19:55687388..55690294,2	K562	blood:
32	chr19:55623549..55625871-chr19:55627412..55630421,4	K562	blood:
33	chr19:55627139..55630124-chr19:55683805..55687284,3	K562	blood:
34	chr19:55628586..55629129-chr8:42752124..42752980,2	Hela-S3	cervix:
35	chr19:55625474..55630122-chr19:55917760..55920694,6	K562	blood:
36	chr19:55586694..55588416-chr19:55627713..55629753,2	MCF-7	breast:
37	chr19:55627842..55630893-chr19:56150877..56153462,3	MCF-7	breast:
38	chr19:55626366..55629144-chr19:56151698..56154505,2	MCF-7	breast:
39	chr19:55592215..55594143-chr19:55627542..55630136,2	MCF-7	breast:
40	chr19:55627863..55630542-chr19:55666165..55668037,2	K562	blood:

No data

Variant related genes	Relation type
PPP1R12C	TF binding region
PPP1R12C	CpG island
ENSG00000125503	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000120925	Chromatin interaction
ENSG00000091127	Chromatin interaction
ENSG00000170889	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000223660	Chromatin interaction
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10401227	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1151617	0.81[EUR][1000 genomes]
rs12982674	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12982699	0.94[EUR][1000 genomes]
rs2109067	0.89[ASN][1000 genomes]
rs2532059	0.81[ASN][1000 genomes]
rs34374641	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56350931	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253188	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7259963	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv912449	chr19:55595687-55630425	Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv912450	chr19:55595687-55633043	Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv912452	chr19:55595687-55644325	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	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
6	nsv1055961	chr19:55613727-55644076	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
7	esv1799218	chr19:55617408-55641955	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060034	chr19:55622592-55650097	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
9	esv1850769	chr19:55622909-55641955	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
10	esv3334199	chr19:55627990-55629988	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 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	chr19:55626800-55630200	Active TSS	Fetal Kidney	kidney
2	chr19:55627200-55629800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:55627200-55629800	Active TSS	Aorta	Aorta
4	chr19:55627200-55629800	Active TSS	Ovary	ovary
5	chr19:55627200-55630000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:55627200-55630800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:55627200-55630800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:55627400-55628800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr19:55627400-55628800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:55627400-55629600	Active TSS	Colon Smooth Muscle	Colon
11	chr19:55627400-55629800	Active TSS	HSMMtube	muscle
12	chr19:55627400-55630000	Active TSS	Left Ventricle	heart
13	chr19:55627600-55628800	Active TSS	Right Atrium	heart
14	chr19:55627600-55629400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:55627600-55629400	Active TSS	Fetal Intestine Large	intestine
16	chr19:55627600-55629600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:55627600-55629600	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr19:55627600-55629600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr19:55627600-55629600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr19:55627600-55629600	Active TSS	Fetal Stomach	stomach
21	chr19:55627600-55629600	Active TSS	A549	lung
22	chr19:55627600-55629600	Active TSS	NHDF-Ad	bronchial
23	chr19:55627600-55629600	Active TSS	NHLF	lung
24	chr19:55627600-55629800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:55627600-55629800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr19:55627600-55629800	Active TSS	GM12878-XiMat	blood
27	chr19:55627600-55630000	Active TSS	Rectal Smooth Muscle	rectum
28	chr19:55627600-55630200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:55627600-55630400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:55627600-55630400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:55627600-55630400	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr19:55627600-55630600	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:55627600-55630800	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr19:55627800-55629400	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:55627800-55629600	Active TSS	Small Intestine	intestine
36	chr19:55627800-55629600	Active TSS	HSMM	muscle
37	chr19:55627800-55629600	Active TSS	NH-A	brain
38	chr19:55627800-55629800	Active TSS	Brain Substantia Nigra	brain
39	chr19:55627800-55629800	Active TSS	Lung	lung
40	chr19:55627800-55629800	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr19:55627800-55630200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:55627800-55630400	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr19:55627800-55630600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:55628000-55629200	Active TSS	Fetal Brain Male	brain
45	chr19:55628000-55629400	Active TSS	Placenta Amnion	Placenta Amnion
46	chr19:55628000-55629600	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr19:55628000-55629600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:55628000-55629600	Active TSS	Stomach Mucosa	stomach
49	chr19:55628000-55629600	Active TSS	Dnd41	blood
50	chr19:55628000-55629800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links