Variant report

Variant	rs2950042
Chromosome Location	chr5:89457327-89457328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:89457277-89457581	K562	blood:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
2	YY1	chr5:89457275-89457642	GM12878	blood:	n/a	chr5:89457611-89457620
3	CTCF	chr5:89457320-89457470	HFF-Myc	foreskin:	n/a	n/a
4	RAD21	chr5:89457210-89457695	H1-hESC	embryonic stem cell:	n/a	chr5:89457502-89457521
5	RCOR1	chr5:89457237-89457583	K562	blood:	n/a	n/a
6	YY1	chr5:89457263-89457626	GM12878	blood:	n/a	chr5:89457611-89457620
7	RAD21	chr5:89457293-89457566	GM12878	blood:	n/a	chr5:89457502-89457521
8	CTCF	chr5:89457280-89457430	NHDF-neo	bronchial:	n/a	n/a
9	RAD21	chr5:89457274-89457633	SK-N-SH_RA	brain:	n/a	chr5:89457502-89457521
10	CTCF	chr5:89457313-89457560	HepG2	liver:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
11	RAD21	chr5:89457312-89457591	K562	blood:	n/a	chr5:89457502-89457521
12	CTCF	chr5:89457291-89457674	MCF-7	breast:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
13	YY1	chr5:89457279-89457567	K562	blood:	n/a	n/a
14	RAD21	chr5:89457146-89457844	HCT-116	colon:	n/a	chr5:89457502-89457521
15	MAFF	chr5:89457253-89457454	K562	blood:	n/a	n/a
16	YY1	chr5:89457163-89457639	H1-hESC	embryonic stem cell:	n/a	chr5:89457611-89457620
17	RAD21	chr5:89457115-89457792	HCT-116	colon:	n/a	chr5:89457502-89457521
18	CTCF	chr5:89457320-89457470	WERI-Rb-1	eye:	n/a	n/a
19	FOS	chr5:89457281-89457467	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr5:89457058-89457831	SK-N-SH	brain:	n/a	chr5:89457502-89457521
21	CTCF	chr5:89457320-89457470	MCF-7	breast:	n/a	n/a
22	CTCF	chr5:89457320-89457470	HA-sp	spinal cord:	n/a	n/a
23	CTCF	chr5:89457241-89457613	HCT-116	colon:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
24	CTCF	chr5:89457192-89457757	MCF-7	breast:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
25	GATA2	chr5:89457150-89457510	HUVEC	blood vessel:	n/a	n/a
26	RAD21	chr5:89457205-89457579	A549	lung:	n/a	chr5:89457502-89457521
27	RAD21	chr5:89457271-89457699	A549	lung:	n/a	chr5:89457502-89457521
28	YY1	chr5:89457256-89457642	H1-hESC	embryonic stem cell:	n/a	chr5:89457611-89457620
29	RAD21	chr5:89457288-89457627	GM12878	blood:	n/a	chr5:89457502-89457521
30	YY1	chr5:89457325-89457684	ECC-1	luminal epithelium:	n/a	chr5:89457611-89457620
31	RAD21	chr5:89457253-89457716	MCF-7	breast:	n/a	chr5:89457502-89457521
32	UBTF	chr5:89457291-89457471	K562	blood:	n/a	n/a
33	CTCF	chr5:89457300-89457450	GM12865	blood:	n/a	n/a
34	REST	chr5:89457319-89457746	PFSK-1	brain:	n/a	n/a
35	CTCF	chr5:89457272-89457648	GM12878	blood:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
36	RAD21	chr5:89457261-89457662	SK-N-SH_RA	brain:	n/a	chr5:89457502-89457521
37	RAD21	chr5:89457245-89457619	HepG2	liver:	n/a	chr5:89457502-89457521
38	RAD21	chr5:89457308-89457605	HepG2	liver:	n/a	chr5:89457502-89457521
39	YY1	chr5:89457234-89457574	K562	blood:	n/a	n/a
40	REST	chr5:89457315-89457577	K562	blood:	n/a	n/a
41	RAD21	chr5:89457178-89457699	H1-hESC	embryonic stem cell:	n/a	chr5:89457502-89457521
42	CTCF	chr5:89457217-89457729	HCT-116	colon:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
43	YY1	chr5:89457308-89457601	GM12891	blood:	n/a	n/a
44	SMC3	chr5:89457294-89457645	GM12878	blood:	n/a	n/a
45	CTCF	chr5:89457271-89457605	H1-hESC	embryonic stem cell:	n/a	chr5:89457504-89457522 chr5:89457506-89457519 chr5:89457499-89457520
46	SMC3	chr5:89457112-89457684	SK-N-SH	brain:	n/a	n/a
47	RAD21	chr5:89457118-89457770	MCF-7	breast:	n/a	chr5:89457502-89457521
48	REST	chr5:89457269-89457604	PFSK-1	brain:	n/a	n/a
49	HDAC2	chr5:89457258-89457595	MCF-7	breast:	n/a	n/a
50	RAD21	chr5:89457254-89457583	GM12878	blood:	n/a	chr5:89457502-89457521

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:88025172..88025905-chr5:89457296..89457865,2	MCF-7	breast:
2	chr5:89225139..89225642-chr5:89457055..89457700,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248555	TF binding region
ENSG00000081189	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2910778	1.00[EUR][1000 genomes]
rs2910779	1.00[EUR][1000 genomes]
rs2910781	1.00[EUR][1000 genomes]
rs2920519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2937824	1.00[EUR][1000 genomes]
rs2950040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2950043	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2950048	1.00[EUR][1000 genomes]
rs2973362	1.00[EUR][1000 genomes]
rs2973404	1.00[EUR][1000 genomes]
rs4560581	1.00[EUR][1000 genomes]
rs58643068	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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	50 gene(s)	inside rSNPs	diseases
5	nsv882362	chr5:89437963-89604380	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3336986	chr5:89450723-89482244	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv830391	chr5:89456582-89641195	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89456800-89457600	Enhancers	Ovary	ovary
2	chr5:89456800-89457600	Enhancers	Stomach Mucosa	stomach
3	chr5:89457000-89457600	Enhancers	Pancreas	Pancrea
4	chr5:89457000-89457600	Enhancers	Right Atrium	heart
5	chr5:89457000-89457600	Enhancers	Spleen	Spleen
6	chr5:89457200-89457400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:89457200-89457600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:89457200-89457600	Enhancers	Adipose Nuclei	Adipose
9	chr5:89457200-89458400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:89457200-89460000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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