Variant report

Variant	rs5003265
Chromosome Location	chr6:29344036-29344037
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	chr6:29343857-29344197	ECC-1	luminal epithelium:	n/a	chr6:29343951-29343970
2	CTCF	chr6:29343920-29344070	WERI-Rb-1	eye:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
3	RAD21	chr6:29343858-29344286	SK-N-SH	brain:	n/a	chr6:29343951-29343970
4	RAD21	chr6:29343758-29344127	MCF-7	breast:	n/a	chr6:29343951-29343970
5	CTCF	chr6:29343894-29344096	A549	lung:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
6	CTCF	chr6:29343900-29344050	SAEC	small airway:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
7	CTCF	chr6:29343908-29344052	Hela-S3	cervix:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
8	RAD21	chr6:29343871-29344078	HepG2	liver:	n/a	chr6:29343951-29343970
9	CTCF	chr6:29343920-29344070	HCPEpiC	choroid plexus:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
10	CTCF	chr6:29343900-29344050	HMEC	breast:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
11	SMC3	chr6:29343730-29344143	GM12878	blood:	n/a	n/a
12	CTCF	chr6:29343822-29344082	K562	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
13	RAD21	chr6:29343713-29344272	HCT-116	colon:	n/a	chr6:29343951-29343970
14	CTCF	chr6:29343920-29344070	HCT-116	colon:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
15	CTCF	chr6:29343900-29344050	HEEpiC	esophagus:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
16	CTCF	chr6:29343945-29344038	GM10248	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
17	RAD21	chr6:29343760-29344097	SK-N-SH_RA	brain:	n/a	chr6:29343951-29343970
18	CTCF	chr6:29343707-29344164	MCF-7	breast:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
19	TBP	chr6:29343970-29344142	GM12878	blood:	n/a	n/a
20	CTCF	chr6:29343940-29344060	Gliobla	brain:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
21	RAD21	chr6:29343699-29344172	HepG2	liver:	n/a	chr6:29343951-29343970
22	CTCF	chr6:29343664-29344257	SK-N-SH	brain:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
23	CTCF	chr6:29343885-29344064	HUVEC	blood vessel:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
24	CTCF	chr6:29343900-29344050	MCF-7	breast:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
25	CTCF	chr6:29343933-29344041	MCF-7	breast:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
26	RAD21	chr6:29343853-29344047	GM12878	blood:	n/a	chr6:29343951-29343970
27	CTCF	chr6:29343900-29344050	GM12875	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
28	CTCF	chr6:29343942-29344056	NHEK	skin:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
29	CTCF	chr6:29343936-29344061	GM10266	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
30	RAD21	chr6:29343808-29344144	GM12878	blood:	n/a	chr6:29343951-29343970
31	CTCF	chr6:29343900-29344050	GM12865	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
32	CTCF	chr6:29343918-29344048	LNCaP	prostate:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
33	CTCF	chr6:29343904-29344050	LNCaP	prostate:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
34	RAD21	chr6:29343921-29344091	Hela-S3	cervix:	n/a	chr6:29343951-29343970
35	CTCF	chr6:29343884-29344055	HepG2	liver:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
36	CTCF	chr6:29343920-29344070	HRPEpiC	eye:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
37	CTCF	chr6:29343858-29344071	K562	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
38	CTCF	chr6:29343920-29344070	RPTEC	kidney:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
39	CTCF	chr6:29343724-29344261	HCT-116	colon:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
40	ZNF143	chr6:29343809-29344104	GM12878	blood:	n/a	n/a
41	CTCF	chr6:29343940-29344090	GM12878	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
42	RAD21	chr6:29343790-29344176	H1-hESC	embryonic stem cell:	n/a	chr6:29343951-29343970
43	CTCF	chr6:29343900-29344050	HMF	breast:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
44	CTCF	chr6:29343940-29344090	HepG2	liver:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
45	RAD21	chr6:29343644-29344183	HCT-116	colon:	n/a	chr6:29343951-29343970
46	CTCF	chr6:29343940-29344090	GM12865	blood:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
47	CTCF	chr6:29343848-29344044	H1-hESC	embryonic stem cell:	n/a	chr6:29343952-29343973 chr6:29343950-29343968
48	RAD21	chr6:29343761-29344080	A549	lung:	n/a	chr6:29343951-29343970
49	RAD21	chr6:29343835-29344236	HepG2	liver:	n/a	chr6:29343951-29343970
50	CTCF	chr6:29343914-29344047	Medullo	brain:	n/a	chr6:29343952-29343973 chr6:29343950-29343968

No.	Distal block	Cell Line	Cell type
1	chr6:29343538..29344515-chr6:29556985..29557870,6	MCF-7	breast:
2	chr6:29343942..29344473-chr6:29556992..29557505,2	MCF-7	breast:
3	chr6:29343821..29344378-chr6:29664074..29664947,2	MCF-7	breast:

Variant related genes	Relation type
OR12D3	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28359953	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3117441	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5003264	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5003266	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5003267	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1020683	chr6:29225146-29353408	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv830624	chr6:29274525-29445565	Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv966676	chr6:29326915-29365789	Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv883527	chr6:29342825-29354799	Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv519453	chr6:29343355-29351873	Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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