Variant report

Variant	rs55991920
Chromosome Location	chr5:42894509-42894510
allele	C/T
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	chr5:42894256-42894627	K562	blood:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
2	CTCF	chr5:42894360-42894510	AG09319	gingival:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
3	GABPA	chr5:42894214-42894603	H1-hESC	embryonic stem cell:	n/a	n/a
4	GABPA	chr5:42894327-42894680	K562	blood:	n/a	n/a
5	CTCF	chr5:42894360-42894510	NHEK	skin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
6	CTCF	chr5:42894373-42894509	NHEK	skin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
7	CTCF	chr5:42894328-42894524	GM19238	blood:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
8	CTCF	chr5:42894380-42894530	HFF-Myc	foreskin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
9	CTCF	chr5:42894331-42894532	ProgFib	skin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
10	CTCF	chr5:42894380-42894530	SK-N-SH_RA	brain:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
11	CTCF	chr5:42894460-42894610	WI-38	lung:	n/a	n/a
12	GTF2F1	chr5:42894263-42894556	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr5:42894277-42894516	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr5:42894325-42894546	Fibrobl	skin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
15	CTCF	chr5:42894380-42894530	HCPEpiC	choroid plexus:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
16	CTCF	chr5:42894172-42894641	H1-hESC	embryonic stem cell:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
17	MAX	chr5:42894230-42894610	K562	blood:	n/a	n/a
18	ZNF143	chr5:42894263-42894614	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr5:42894340-42894530	Gliobla	brain:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
20	CTCF	chr5:42894299-42894555	H1-hESC	embryonic stem cell:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
21	CTCF	chr5:42894360-42894510	HCPEpiC	choroid plexus:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
22	CTCF	chr5:42894360-42894510	HFF	foreskin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
23	CTCF	chr5:42894360-42894510	HPAF	blood vessel:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
24	CTCF	chr5:42894354-42894520	MCF-7	breast:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
25	TEAD4	chr5:42894263-42894521	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr5:42894153-42894622	H1-hESC	embryonic stem cell:	n/a	chr5:42894417-42894436 chr5:42894419-42894431 chr5:42894420-42894433
27	CTCF	chr5:42894380-42894530	Caco-2	colon:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
28	CTCF	chr5:42894360-42894510	GM12874	blood:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
29	CTCF	chr5:42894380-42894530	HUVEC	blood vessel:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
30	CTCF	chr5:42894355-42894527	HepG2	liver:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
31	ELF1	chr5:42894275-42894662	SK-N-SH	brain:	n/a	chr5:42894444-42894453
32	CTCF	chr5:42894420-42894570	NHEK	skin:	n/a	chr5:42894420-42894436
33	CTCF	chr5:42894367-42894518	GM12878	blood:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
34	CTCF	chr5:42894400-42894550	HRE	kidney:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
35	NANOG	chr5:42894237-42894524	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr5:42894360-42894510	HCT-116	colon:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
37	CTCF	chr5:42894440-42894590	MCF-7	breast:	n/a	n/a
38	CTCF	chr5:42894380-42894530	NHDF-neo	bronchial:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
39	CTCF	chr5:42894380-42894530	HCFaa	heart:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
40	CTCF	chr5:42894400-42894550	GM12873	blood:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
41	CTCF	chr5:42894360-42894510	HepG2	liver:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
42	CTCF	chr5:42894460-42894610	HRPEpiC	eye:	n/a	n/a
43	CTCF	chr5:42894380-42894530	GM12865	blood:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
44	TBP	chr5:42894240-42894599	H1-hESC	embryonic stem cell:	n/a	n/a
45	MYC	chr5:42894291-42894550	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr5:42894360-42894510	Hela-S3	cervix:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
47	CBX3	chr5:42894229-42894600	K562	blood:	n/a	n/a
48	BRCA1	chr5:42894337-42894557	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr5:42894400-42894550	AG10803	skin:	n/a	chr5:42894419-42894437 chr5:42894420-42894436
50	CTCF	chr5:42894335-42894534	MCF-7	breast:	n/a	chr5:42894419-42894437 chr5:42894420-42894436

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42887211..42889280-chr5:42893252..42895006,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249092	TF binding region
ENSG00000250722	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs4082200	0.95[AFR][1000 genomes]
rs59185684	1.00[AFR][1000 genomes]
rs60120785	0.85[AFR][1000 genomes]
rs73751276	1.00[AFR][1000 genomes]
rs73751279	1.00[AFR][1000 genomes]
rs73751280	1.00[AFR][1000 genomes]
rs73751284	1.00[AFR][1000 genomes]
rs73751286	0.95[AFR][1000 genomes]
rs73751287	1.00[AFR][1000 genomes]
rs73751288	0.95[AFR][1000 genomes]
rs73751290	0.95[AFR][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	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
2	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
3	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
5	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
7	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active 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	309 gene(s)	inside rSNPs	diseases
8	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
9	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv980936	chr5:42894375-42930741	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42894200-42894600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr5:42894200-42894600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:42894200-42894600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:42894200-42894600	Active TSS	Left Ventricle	heart
5	chr5:42894200-42894600	Enhancers	Pancreas	Pancrea
6	chr5:42894400-42894600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr5:42894400-42894600	Enhancers	Psoas Muscle	Psoas
8	chr5:42894400-42894600	Enhancers	K562	blood
9	chr5:42894400-42902000	Weak transcription	Right Atrium	heart

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