Variant report

Variant	rs12083959
Chromosome Location	chr1:152370116-152370117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:152370103-152370214	GM19239	blood:	n/a	n/a
2	CTCF	chr1:152370100-152370250	A549	lung:	n/a	n/a
3	CTCF	chr1:152370099-152370260	GM12891	blood:	n/a	n/a
4	CTCF	chr1:152370020-152370170	AG10803	skin:	n/a	n/a
5	CTCF	chr1:152370060-152370210	BE2_C	brain:	n/a	n/a
6	CTCF	chr1:152370066-152370253	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr1:152370080-152370230	HepG2	liver:	n/a	n/a
8	CTCF	chr1:152370100-152370250	RPTEC	kidney:	n/a	n/a
9	CTCF	chr1:152370070-152370229	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr1:152370080-152370230	WERI-Rb-1	eye:	n/a	n/a
11	CTCF	chr1:152370065-152370267	LNCaP	prostate:	n/a	n/a
12	CTCF	chr1:152370060-152370210	HMF	breast:	n/a	n/a
13	RAD21	chr1:152370030-152370258	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr1:152370106-152370210	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr1:152370026-152370289	MCF-7	breast:	n/a	n/a
16	CTCF	chr1:152370080-152370230	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr1:152370008-152370295	Gliobla	brain:	n/a	n/a
18	CTCF	chr1:152370082-152370234	HepG2	liver:	n/a	n/a
19	CTCF	chr1:152369833-152370431	MCF-7	breast:	n/a	n/a
20	CTCF	chr1:152370080-152370230	AG10803	skin:	n/a	n/a
21	RAD21	chr1:152370004-152370351	MCF-7	breast:	n/a	n/a
22	CTCF	chr1:152370070-152370278	MCF-7	breast:	n/a	n/a
23	CTCF	chr1:152370071-152370254	Fibrobl	skin:	n/a	n/a
24	RAD21	chr1:152370039-152370231	K562	blood:	n/a	n/a
25	CTCF	chr1:152370100-152370250	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr1:152370100-152370250	GM12875	blood:	n/a	n/a
27	CTCF	chr1:152370064-152370243	ProgFib	skin:	n/a	n/a
28	CTCF	chr1:152370080-152370230	GM12868	blood:	n/a	n/a
29	CTCF	chr1:152370080-152370230	RPTEC	kidney:	n/a	n/a
30	CTCF	chr1:152369997-152370284	A549	lung:	n/a	n/a
31	CTCF	chr1:152370080-152370230	HRPEpiC	eye:	n/a	n/a
32	CTCF	chr1:152370040-152370190	SAEC	small airway:	n/a	n/a
33	CTCF	chr1:152370100-152370250	K562	blood:	n/a	n/a
34	CTCF	chr1:152370068-152370231	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr1:152370040-152370190	HPAF	blood vessel:	n/a	n/a
36	CTCF	chr1:152370080-152370230	HMF	breast:	n/a	n/a
37	CTCF	chr1:152370100-152370250	GM12864	blood:	n/a	n/a
38	CTCF	chr1:152370100-152370250	HBMEC	blood vessel:	n/a	n/a
39	CTCF	chr1:152370060-152370210	GM12871	blood:	n/a	n/a
40	CTCF	chr1:152370106-152370230	GM12892	blood:	n/a	n/a
41	CTCF	chr1:152370063-152370306	HepG2	liver:	n/a	n/a
42	CTCF	chr1:152370080-152370230	Caco-2	colon:	n/a	n/a
43	CTCF	chr1:152370080-152370230	K562	blood:	n/a	n/a
44	CTCF	chr1:152370060-152370210	MCF-7	breast:	n/a	n/a
45	RAD21	chr1:152370025-152370246	HepG2	liver:	n/a	n/a
46	SMC3	chr1:152369940-152370368	SK-N-SH	brain:	n/a	n/a
47	CTCF	chr1:152370040-152370190	WERI-Rb-1	eye:	n/a	n/a
48	CTCF	chr1:152369889-152370474	MCF-7	breast:	n/a	n/a
49	CTCF	chr1:152370060-152370210	GM12873	blood:	n/a	n/a
50	CTCF	chr1:152370040-152370190	GM12874	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152369874..152370523-chr1:152423403..152423977,2	MCF-7	breast:
2	chr1:152369672..152370659-chr1:152413047..152413901,4	MCF-7	breast:
3	chr1:152368385..152370359-chr1:152413395..152416053,2	MCF-7	breast:
4	chr1:152369802..152370305-chr1:152430586..152431135,2	K562	blood:
5	chr1:152369903..152370605-chr1:152413321..152413987,3	MCF-7	breast:
6	chr1:152369716..152370381-chr10:53149139..53149795,2	MCF-7	breast:

No data

Variant related genes	Relation type
HMGN3P1	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11204983	1.00[EUR][1000 genomes]
rs12057680	1.00[EUR][1000 genomes]
rs12060296	1.00[EUR][1000 genomes]
rs12066296	1.00[EUR][1000 genomes]
rs12067755	1.00[EUR][1000 genomes]
rs12078392	1.00[EUR][1000 genomes]
rs12079093	1.00[YRI][hapmap]
rs16834174	1.00[EUR][1000 genomes]
rs1858481	1.00[EUR][1000 genomes]
rs28655434	1.00[EUR][1000 genomes]
rs3120654	1.00[EUR][1000 genomes]
rs3126087	1.00[EUR][1000 genomes]
rs3126093	1.00[EUR][1000 genomes]
rs3134871	1.00[EUR][1000 genomes]
rs56106510	1.00[EUR][1000 genomes]
rs56244386	1.00[EUR][1000 genomes]
rs566973	1.00[EUR][1000 genomes]
rs57272962	1.00[EUR][1000 genomes]
rs57934636	1.00[EUR][1000 genomes]
rs58788896	1.00[EUR][1000 genomes]
rs58823849	1.00[EUR][1000 genomes]
rs58935238	1.00[EUR][1000 genomes]
rs60095860	1.00[EUR][1000 genomes]
rs60179982	1.00[EUR][1000 genomes]
rs60709044	1.00[EUR][1000 genomes]
rs60963018	1.00[EUR][1000 genomes]
rs61230786	1.00[EUR][1000 genomes]
rs73003080	1.00[EUR][1000 genomes]
rs73003789	1.00[EUR][1000 genomes]
rs73004841	1.00[EUR][1000 genomes]
rs73004845	1.00[EUR][1000 genomes]
rs73004848	1.00[EUR][1000 genomes]
rs73004856	1.00[EUR][1000 genomes]
rs73004882	1.00[EUR][1000 genomes]
rs73004888	1.00[EUR][1000 genomes]
rs73006958	1.00[EUR][1000 genomes]
rs73006962	1.00[EUR][1000 genomes]
rs733439	1.00[EUR][1000 genomes]
rs74127885	1.00[EUR][1000 genomes]
rs74127887	1.00[EUR][1000 genomes]
rs74127894	1.00[EUR][1000 genomes]
rs74127895	1.00[EUR][1000 genomes]
rs74127917	1.00[EUR][1000 genomes]
rs74127918	1.00[EUR][1000 genomes]
rs74128280	1.00[EUR][1000 genomes]
rs74129414	1.00[EUR][1000 genomes]
rs74129429	1.00[EUR][1000 genomes]
rs74129447	1.00[EUR][1000 genomes]
rs74129458	1.00[EUR][1000 genomes]
rs74129459	1.00[EUR][1000 genomes]
rs74129463	1.00[EUR][1000 genomes]
rs74129464	1.00[EUR][1000 genomes]
rs74129466	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No data

Quick Search:

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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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