Variant report

Variant	rs2886518
Chromosome Location	chr3:61544984-61544985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:61544840-61544990	HEK293	kidney:	n/a	n/a
2	CTCF	chr3:61544840-61544990	HA-sp	spinal cord:	n/a	n/a
3	CTCF	chr3:61544960-61545110	HRE	kidney:	n/a	n/a
4	CTCF	chr3:61544840-61544990	HPF	lung:	n/a	n/a
5	CTCF	chr3:61544774-61545076	GM12878	blood:	n/a	n/a
6	CTCF	chr3:61544860-61545010	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr3:61544840-61544990	AG04449	skin:	n/a	n/a
8	RAD21	chr3:61544798-61545060	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr3:61544840-61544990	HCT-116	colon:	n/a	n/a
10	CTCF	chr3:61544900-61545050	NHLF	lung:	n/a	n/a
11	CTCF	chr3:61544840-61544990	RPTEC	kidney:	n/a	n/a
12	CTCF	chr3:61544840-61544990	HCPEpiC	choroid plexus:	n/a	n/a
13	CTCF	chr3:61544864-61544993	HepG2	liver:	n/a	n/a
14	CTCF	chr3:61544860-61545010	HepG2	liver:	n/a	n/a
15	CTCF	chr3:61544840-61544990	AG10803	skin:	n/a	n/a
16	CTCF	chr3:61544860-61545010	HCFaa	heart:	n/a	n/a
17	CTCF	chr3:61544900-61545050	AG04450	lung:	n/a	n/a
18	CTCF	chr3:61544860-61545010	HA-sp	spinal cord:	n/a	n/a
19	CTCF	chr3:61544796-61545098	IMR90	lung:	n/a	n/a
20	CTCF	chr3:61544860-61545010	RPTEC	kidney:	n/a	n/a
21	SMC3	chr3:61544786-61545018	HepG2	liver:	n/a	n/a
22	CTCF	chr3:61544935-61544987	Kidney_OC	kidney:	n/a	n/a
23	CTCF	chr3:61544840-61544990	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr3:61544860-61545010	HVMF	connective:	n/a	n/a
25	CTCF	chr3:61544840-61544990	AoAF	blood vessel:	n/a	n/a
26	CTCF	chr3:61544860-61545010	AG04449	skin:	n/a	n/a
27	CTCF	chr3:61544900-61545050	HCM	heart:	n/a	n/a
28	CTCF	chr3:61544840-61544990	HVMF	connective:	n/a	n/a
29	CTCF	chr3:61544880-61545030	GM12874	blood:	n/a	n/a
30	CTCF	chr3:61544940-61545090	AG04450	lung:	n/a	n/a
31	POLR2A	chr3:61544738-61545491	HepG2	liver:	n/a	n/a
32	CTCF	chr3:61544840-61544990	AG09309	skin:	n/a	n/a
33	CTCF	chr3:61544873-61545005	HUVEC	blood vessel:	n/a	n/a
34	CTCF	chr3:61544880-61545030	WERI-Rb-1	eye:	n/a	n/a
35	CTCF	chr3:61544840-61544990	HMEC	breast:	n/a	n/a
36	CTCF	chr3:61544960-61545110	HFF-Myc	foreskin:	n/a	n/a
37	CTCF	chr3:61544920-61545070	NHDF-neo	bronchial:	n/a	n/a
38	CTCF	chr3:61544840-61544990	HUVEC	blood vessel:	n/a	n/a
39	RAD21	chr3:61544734-61545013	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr3:61544860-61545010	AG09309	skin:	n/a	n/a
41	CTCF	chr3:61544840-61544990	SK-N-SH_RA	brain:	n/a	n/a
42	CTCF	chr3:61544860-61545007	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:61544864-61554855	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr3:61544880-61545030	HPF	lung:	n/a	n/a
45	RAD21	chr3:61544817-61545056	HepG2	liver:	n/a	n/a
46	CTCF	chr3:61544840-61544990	BJ	skin:	n/a	n/a
47	CTCF	chr3:61544860-61545010	HFF	foreskin:	n/a	n/a
48	CTCF	chr3:61544840-61544990	HMF	breast:	n/a	n/a
49	CTCF	chr3:61544840-61544990	HAc	cerebellar:	n/a	n/a
50	CTCF	chr3:61544840-61544990	HPAF	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61541363..61545409-chr3:61545583..61548750,5	MCF-7	breast:
2	chr3:61538544..61540472-chr3:61544545..61547220,2	K562	blood:

No data

Variant related genes	Relation type
PTPRG	TF binding region
ENSG00000144724	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11713144	0.82[ASN][1000 genomes]
rs13059759	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2365956	0.80[ASN][1000 genomes]
rs2886520	0.88[ASN][1000 genomes]
rs35668148	0.89[ASN][1000 genomes]
rs62268713	0.86[ASN][1000 genomes]
rs6789675	0.89[ASN][1000 genomes]
rs7638985	1.00[ASN][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	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1841066	chr3:61534766-61550452	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv3351193	chr3:61544484-61545022	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61523200-61545000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:61542200-61545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:61543800-61545400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:61544600-61545000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:61544600-61545400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:61544800-61545000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:61544800-61545200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr3:61544800-61545200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:61544800-61545200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:61544800-61545400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:61544800-61545400	Enhancers	Placenta	Placenta

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