Variant report

Variant	rs60340472
Chromosome Location	chr1:162006751-162006752
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	RAD21	chr1:162006720-162007120	Hela-S3	cervix:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
2	SMC3	chr1:162005711-162007342	SK-N-SH	brain:	n/a	chr1:162007028-162007035 chr1:162006909-162006923
3	RAD21	chr1:162006658-162007143	HepG2	liver:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
4	RAD21	chr1:162006620-162007221	A549	lung:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
5	RAD21	chr1:162006656-162007154	SK-N-SH_RA	brain:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
6	ZNF384	chr1:162006662-162007307	GM12878	blood:	n/a	n/a
7	RAD21	chr1:162006644-162007104	A549	lung:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
8	CTCF	chr1:162006601-162007284	HCT-116	colon:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
9	CTCF	chr1:162006657-162007210	K562	blood:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
10	RAD21	chr1:162006693-162007306	IMR90	lung:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
11	SP1	chr1:162006646-162007113	A549	lung:	n/a	n/a
12	CTCF	chr1:162006633-162007299	HCT-116	colon:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
13	RAD21	chr1:162006693-162007157	H1-hESC	embryonic stem cell:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
14	RAD21	chr1:162006652-162007226	ECC-1	luminal epithelium:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
15	CTCF	chr1:162006676-162007190	MCF-7	breast:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
16	SMC3	chr1:162006738-162007153	GM12878	blood:	n/a	chr1:162007028-162007035 chr1:162006909-162006923
17	CTCF	chr1:162006453-162007488	SK-N-SH	brain:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
18	RAD21	chr1:162006692-162007091	ECC-1	luminal epithelium:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
19	ZNF384	chr1:162006486-162007122	K562	blood:	n/a	n/a
20	RAD21	chr1:162006614-162007293	HCT-116	colon:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
21	CTCF	chr1:162006745-162007042	A549	lung:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
22	SMC3	chr1:162006735-162007090	HepG2	liver:	n/a	chr1:162007028-162007035 chr1:162006909-162006923
23	RAD21	chr1:162006739-162007099	A549	lung:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
24	CTCF	chr1:162006692-162007038	A549	lung:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
25	RAD21	chr1:162006720-162007121	HepG2	liver:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
26	RAD21	chr1:162006582-162007236	MCF-7	breast:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
27	CTCF	chr1:162006600-162007371	A549	lung:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
28	RAD21	chr1:162006724-162007093	GM12878	blood:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
29	SMC3	chr1:162006722-162007142	Hela-S3	cervix:	n/a	chr1:162007028-162007035 chr1:162006909-162006923
30	CTCF	chr1:162006717-162007151	GM12878	blood:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
31	CTCF	chr1:162006711-162007119	IMR90	lung:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
32	RAD21	chr1:162005759-162007370	SK-N-SH	brain:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
33	RAD21	chr1:162006662-162007162	H1-hESC	embryonic stem cell:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
34	CTCF	chr1:162006716-162007136	K562	blood:	n/a	chr1:162006902-162006923 chr1:162006907-162006925 chr1:162006908-162006924
35	RAD21	chr1:162006749-162007080	K562	blood:	n/a	chr1:162006914-162006923 chr1:162006905-162006924
36	RAD21	chr1:162006457-162007240	HCT-116	colon:	n/a	chr1:162006914-162006923 chr1:162006905-162006924

No.	Distal block	Cell Line	Cell type
1	chr1:161732981..161734219-chr1:162006454..162007424,4	MCF-7	breast:
2	chr1:161762367..161763113-chr1:162006230..162006967,3	K562	blood:
3	chr1:161834761..161835393-chr1:162006439..162007058,2	MCF-7	breast:
4	chr1:161874943..161875452-chr1:162006466..162007002,2	MCF-7	breast:
5	chr1:161874812..161875645-chr1:162006504..162007840,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227818	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16842397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17454327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6666546	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74127517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh 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	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS 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 target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:162004800-162007200	Enhancers	NHEK	skin
2	chr1:162004800-162007400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:162005200-162006800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:162005400-162007000	Weak transcription	Psoas Muscle	Psoas
5	chr1:162005400-162008000	Enhancers	HepG2	liver
6	chr1:162005600-162007000	Weak transcription	Right Atrium	heart
7	chr1:162005600-162010200	Weak transcription	Aorta	Aorta
8	chr1:162006200-162007000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:162006200-162007400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:162006400-162006800	Enhancers	Fetal Muscle Trunk	muscle
11	chr1:162006400-162007400	Enhancers	Fetal Muscle Leg	muscle
12	chr1:162006400-162009400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:162006600-162007600	Weak transcription	H9 Cell Line	embryonic stem cell

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