Variant report

Variant	rs28623177
Chromosome Location	chr15:53086729-53086730
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr15:53086487-53086824	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr15:53086521-53088992	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD2	chr15:53086552-53087160	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr15:53086576-53086753	H1-hESC	embryonic stem cell:	n/a	n/a
5	BACH1	chr15:53086711-53087039	H1-hESC	embryonic stem cell:	n/a	n/a
6	SUZ12	chr15:53086684-53088933	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:53086726-53086776	HMEC	breast:	n/a
2	chr15:53086726-53086776	NB4	blood:	n/a
3	chr15:53086726-53086776	MCF-7	breast:	n/a
4	chr15:53086726-53086776	PANC-1	pancreas:	n/a
5	chr15:53086726-53086776	AG04449	skin:	fetal
6	chr15:53086726-53086776	BJ	skin:	n/a
7	chr15:53086726-53086776	H1-hESC	embryonic stem cell:	embryo
8	chr15:53086726-53086776	Jurkat	blood:	n/a
9	chr15:53086726-53086776	SK-N-SH_RA	brain:	n/a
10	chr15:53086726-53086776	AG09309	skin:	n/a
11	chr15:53086726-53086776	GM12891	blood:	n/a
12	chr15:53086726-53086776	CMK	blood:	n/a
13	chr15:53086726-53086776	HAEpiC	amniotic membrane:	n/a
14	chr15:53086726-53086776	Hepatocyte	liver:	n/a
15	chr15:53086726-53086776	PFSK-1	brain:	n/a
16	chr15:53086726-53086776	HNPCEpiC	eye:	n/a
17	chr15:53086726-53086776	HCT-116	colon:	n/a
18	chr15:53086726-53086776	HEEpiC	esophagus:	n/a
19	chr15:53086726-53086776	K562	blood:	n/a
20	chr15:53086726-53086776	AG04450	lung:	fetal
21	chr15:53086726-53086776	HPAEpiC	pulmonary alveolar:	n/a
22	chr15:53086726-53086776	ProgFib	skin:	n/a
23	chr15:53086726-53086776	GM12878	blood:	n/a
24	chr15:53086726-53086776	LNCaP	prostate:	n/a
25	chr15:53086726-53086776	HRE	kidney:	n/a
26	chr15:53086726-53086776	SKMC	muscle:	n/a
27	chr15:53086726-53086776	AoSMC	blood vessel:	n/a
28	chr15:53086726-53086776	BE2_C	brain:	n/a
29	chr15:53086726-53086776	HCPEpiC	choroid plexus:	n/a
30	chr15:53086726-53086776	HIPEpiC	eye:	n/a
31	chr15:53086726-53086776	NH-A	brain:	n/a
32	chr15:53086726-53086776	GM06990	blood:	n/a
33	chr15:53086726-53086776	HCF	heart:	n/a
34	chr15:53086726-53086776	NHDF-neo	bronchial:	n/a
35	chr15:53086726-53086776	AG09319	gingival:	n/a
36	chr15:53086726-53086776	HEK293	kidney:	embryo
37	chr15:53086726-53086776	U87	brain:	n/a
38	chr15:53086726-53086776	AG10803	skin:	n/a
39	chr15:53086726-53086776	ovcar-3	ovarian:	n/a
40	chr15:53086726-53086776	GM19239	blood:	n/a
41	chr15:53086726-53086776	HL-60	blood:	n/a
42	chr15:53086726-53086776	Caco-2	colon:	n/a
43	chr15:53086726-53086776	SK-N-MC	brain:	n/a
44	chr15:53086726-53086776	GM12892	blood:	n/a
45	chr15:53086726-53086776	IMR90	lung:	fetal
46	chr15:53086726-53086776	HUVEC	blood vessel:	n/a
47	chr15:53086726-53086776	NT2-D1	testis:	n/a
48	chr15:53086726-53086776	HRCEpiC	kidney:	n/a
49	chr15:53086726-53086776	HepG2	liver:	n/a
50	chr15:53086726-53086776	SAEC	small airway:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK6-11	chr15:53086548-53087549	XLOC_011257

No data

Variant related genes	Relation type
ONECUT1	TF binding region
ONECUT1	CpG island

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16965168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16965288	1.00[AMR][1000 genomes]
rs61745272	1.00[AMR][1000 genomes]
rs7183326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413462	1.00[AMR][1000 genomes]
rs8041658	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53083600-53088400	Weak transcription	Pancreas	Pancrea
2	chr15:53083600-53088600	Weak transcription	Liver	Liver
3	chr15:53084000-53086800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr15:53084000-53086800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr15:53084000-53086800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr15:53084200-53086800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr15:53084200-53086800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:53086000-53086800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:53086600-53086800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr15:53086600-53086800	Bivalent Enhancer	Right Ventricle	heart
11	chr15:53086600-53087200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:53086600-53087400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
13	chr15:53086600-53087800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links