Variant report

Variant	rs7515448
Chromosome Location	chr1:152372035-152372036
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	RAD21	chr1:152371419-152372234	MCF-7	breast:	n/a	chr1:152371728-152371738 chr1:152371723-152371742
2	CTCF	chr1:152371604-152372101	MCF-7	breast:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
3	CTCF	chr1:152371940-152372065	ProgFib	skin:	n/a	n/a
4	CTCF	chr1:152371939-152372073	Gliobla	brain:	n/a	n/a
5	CTCF	chr1:152372020-152372170	GM12864	blood:	n/a	n/a
6	CTCF	chr1:152371422-152372339	HCT-116	colon:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
7	RAD21	chr1:152371396-152372188	HCT-116	colon:	n/a	chr1:152371728-152371738 chr1:152371723-152371742
8	CTCF	chr1:152371882-152372094	MCF-7	breast:	n/a	n/a
9	RAD21	chr1:152371511-152372116	HCT-116	colon:	n/a	chr1:152371728-152371738 chr1:152371723-152371742
10	ZNF217	chr1:152371556-152372114	MCF-7	breast:	n/a	n/a
11	CTCF	chr1:152371935-152372036	HepG2	liver:	n/a	n/a
12	CTCF	chr1:152371587-152372097	MCF-7	breast:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
13	CTCF	chr1:152371940-152372090	HRE	kidney:	n/a	n/a
14	CTCF	chr1:152371871-152372100	MCF-7	breast:	n/a	n/a
15	RAD21	chr1:152371502-152372155	MCF-7	breast:	n/a	chr1:152371728-152371738 chr1:152371723-152371742
16	CTCF	chr1:152371521-152372080	T-47D	breast:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
17	POLR2A	chr1:152371907-152372073	GM12878	blood:	n/a	n/a
18	CTCF	chr1:152371934-152372050	Fibrobl	skin:	n/a	n/a
19	CTCF	chr1:152371533-152372113	HepG2	liver:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
20	CTCF	chr1:152371565-152372111	MCF-7	breast:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
21	CTCF	chr1:152371323-152372314	A549	lung:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
22	POLR2A	chr1:152371957-152372055	K562	blood:	n/a	n/a
23	CTCF	chr1:152371495-152372250	MCF-7	breast:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
24	CTCF	chr1:152371414-152372053	SK-N-SH	brain:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
25	CTCF	chr1:152371900-152372050	HBMEC	blood vessel:	n/a	n/a
26	CTCF	chr1:152371589-152372084	A549	lung:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
27	CTCF	chr1:152371338-152372275	HCT-116	colon:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
28	SMC3	chr1:152371316-152372124	SK-N-SH	brain:	n/a	chr1:152371724-152371738 chr1:152371724-152371731
29	CTCF	chr1:152371352-152372247	MCF-7	breast:	n/a	chr1:152371724-152371745 chr1:152371722-152371740 chr1:152371725-152371734
30	CTCF	chr1:152371905-152372041	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152371466..152372490-chr6:79944096..79944688,3	NB4	blood:
2	chr1:152371971..152372478-chr6:79943574..79944555,2	MCF-7	breast:

Variant related genes	Relation type
HMGN3P1	TF binding region
ENSG00000118418	Chromatin interaction

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

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

rs_ID	r²[population]
rs10788835	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888486	0.86[JPT][hapmap]
rs11204982	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204984	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204985	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11204986	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11204987	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11204995	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204996	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204997	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204998	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11301808	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11588022	0.87[ASN][1000 genomes]
rs11803108	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12022217	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12027445	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12029431	0.81[JPT][hapmap]
rs12029633	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032854	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12049036	0.85[JPT][hapmap]
rs12402680	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12403031	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12407319	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12408401	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12568784	0.87[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1858485	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1923493	0.86[JPT][hapmap]
rs1923505	0.90[ASN][1000 genomes]
rs1923506	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933066	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2065954	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2146119	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2275264	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282303	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2525	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3120665	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3120666	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3120667	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3126099	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3753443	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs3753444	0.86[JPT][hapmap]
rs3818831	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829868	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs4285700	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs4378206	0.87[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs45541239	0.90[ASN][1000 genomes]
rs6587668	0.89[ASN][1000 genomes]
rs6679449	0.93[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs6693160	0.89[ASN][1000 genomes]
rs7514696	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521839	0.86[JPT][hapmap];0.95[MEX][hapmap]
rs941935	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9633410	0.80[AMR][1000 genomes];0.90[ASN][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

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