Variant report

Variant	rs11542503
Chromosome Location	chr19:55687413-55687414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr19:55687375-55687781	K562	blood:	n/a	n/a
2	CTCF	chr19:55687339-55687550	MCF-7	breast:	n/a	n/a
3	NR2C2	chr19:55687261-55687840	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr19:55687380-55687530	MCF-7	breast:	n/a	n/a
5	RAD21	chr19:55687303-55687503	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr19:55687390-55687496	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr19:55687300-55687450	A549	lung:	n/a	n/a
8	CTCF	chr19:55687380-55687530	HepG2	liver:	n/a	n/a
9	CTCF	chr19:55687257-55687591	MCF-7	breast:	n/a	n/a
10	CTCF	chr19:55687300-55687450	SAEC	small airway:	n/a	n/a
11	CTCF	chr19:55687340-55687490	AG04449	skin:	n/a	n/a
12	CTCF	chr19:55687340-55687537	MCF-7	breast:	n/a	n/a
13	CTCF	chr19:55687237-55687657	K562	blood:	n/a	n/a
14	CTCF	chr19:55687320-55687470	NHEK	skin:	n/a	n/a
15	MAX	chr19:55687227-55687976	K562	blood:	n/a	chr19:55687727-55687737 chr19:55687726-55687737
16	CTCF	chr19:55687345-55687553	MCF-7	breast:	n/a	n/a
17	CTCF	chr19:55687400-55687550	K562	blood:	n/a	n/a
18	CTCF	chr19:55687300-55687450	GM12878	blood:	n/a	n/a
19	CTCF	chr19:55687320-55687470	SK-N-SH_RA	brain:	n/a	n/a
20	TEAD4	chr19:55687325-55687964	K562	blood:	n/a	n/a
21	POLR2A	chr19:55684256-55687473	K562	blood:	n/a	n/a
22	CTCF	chr19:55687380-55687530	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr19:55687380-55687530	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr19:55687335-55687562	MCF-7	breast:	n/a	n/a
25	CTCF	chr19:55687300-55687450	HMEC	breast:	n/a	n/a
26	CTCF	chr19:55687379-55687475	NHEK	skin:	n/a	n/a
27	RAD21	chr19:55687340-55687495	K562	blood:	n/a	n/a
28	POLR2A	chr19:55687363-55687842	HepG2	liver:	n/a	n/a
29	JUN	chr19:55684455-55688134	K562	blood:	n/a	chr19:55686466-55686475 chr19:55687873-55687887 chr19:55685270-55685279
30	ELF1	chr19:55687307-55687868	K562	blood:	n/a	n/a
31	CTCF	chr19:55687320-55687470	HEK293	kidney:	n/a	n/a
32	CTCF	chr19:55687388-55687475	K562	blood:	n/a	n/a
33	CTCF	chr19:55687340-55687490	WERI-Rb-1	eye:	n/a	n/a
34	CTCF	chr19:55687280-55687866	K562	blood:	n/a	n/a
35	POLR2A	chr19:55685402-55688569	H1-neurons	neurons:	n/a	n/a
36	CTCF	chr19:55687413-55687485	A549	lung:	n/a	n/a
37	MXI1	chr19:55687381-55687862	K562	blood:	n/a	n/a
38	CTCF	chr19:55687340-55687542	MCF-7	breast:	n/a	n/a
39	SMC3	chr19:55687319-55687698	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr19:55687291-55687657	H1-hESC	embryonic stem cell:	n/a	n/a
41	CBX3	chr19:55687377-55687995	K562	blood:	n/a	n/a
42	CTCF	chr19:55687340-55687490	HepG2	liver:	n/a	n/a
43	CTCF	chr19:55687358-55687491	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:55683524..55688236-chr19:55723837..55729899,9	K562	blood:
2	chr19:55686310..55687891-chr19:55719950..55721494,2	K562	blood:
3	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
4	chr19:55684707..55688022-chr19:55908129..55911789,4	K562	blood:
5	chr19:55590426..55594638-chr19:55684228..55687886,4	K562	blood:
6	chr19:55685149..55688070-chr19:55790255..55792658,4	K562	blood:
7	chr19:55624933..55628932-chr19:55685116..55688802,5	K562	blood:
8	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
9	chr19:55592011..55594638-chr19:55684282..55687431,3	K562	blood:
10	chr19:55685793..55687548-chr19:56110126..56112399,2	K562	blood:
11	chr19:55687032..55688994-chr19:55895402..55898104,2	K562	blood:
12	chr19:55626440..55629266-chr19:55687388..55690294,2	K562	blood:
13	chr19:55684986..55687548-chr19:55917710..55920086,4	K562	blood:

No data

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000267577	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000129990	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10426959	1.00[TSI][hapmap]
rs3729707	1.00[ASN][1000 genomes]
rs3859541	1.00[ASN][1000 genomes]
rs59637479	1.00[ASN][1000 genomes]
rs6509928	1.00[ASN][1000 genomes]
rs6509929	1.00[ASN][1000 genomes]
rs6509931	1.00[CHD][hapmap]
rs6509932	1.00[CHD][hapmap]
rs7249445	1.00[ASN][1000 genomes]
rs7249985	1.00[ASN][1000 genomes]
rs7252414	1.00[ASN][1000 genomes]
rs73617692	1.00[ASN][1000 genomes]
rs73617693	1.00[ASN][1000 genomes]
rs73619532	1.00[ASN][1000 genomes]
rs8102415	1.00[ASN][1000 genomes]
rs8102456	1.00[ASN][1000 genomes]
rs8113062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749354	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55685200-55690400	Weak transcription	Gastric	stomach
2	chr19:55685600-55687800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:55685600-55690400	Weak transcription	Pancreas	Pancrea
4	chr19:55685600-55690400	Weak transcription	Right Atrium	heart
5	chr19:55685800-55690200	Weak transcription	Osteobl	bone
6	chr19:55685800-55690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:55686000-55689200	Weak transcription	Hela-S3	cervix
8	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:55686000-55690200	Weak transcription	A549	lung
10	chr19:55686000-55690200	Weak transcription	NHEK	skin
11	chr19:55686200-55688000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:55686200-55689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:55686600-55687800	Flanking Active TSS	K562	blood
14	chr19:55686800-55688000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr19:55686800-55688200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr19:55687000-55687600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:55687000-55689600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:55687200-55689000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:55687200-55689600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:55687400-55688000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
21	chr19:55687400-55689400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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