Variant report

Variant	rs1173077
Chromosome Location	chr1:179220878-179220879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:179220853-179221226	GM12878	blood:	n/a	n/a
2	RAD21	chr1:179220743-179221312	ECC-1	luminal epithelium:	n/a	n/a
3	SMC3	chr1:179220847-179221229	HepG2	liver:	n/a	n/a
4	CTCF	chr1:179220846-179221337	MCF-7	breast:	n/a	n/a
5	RAD21	chr1:179220846-179221248	HepG2	liver:	n/a	n/a
6	RAD21	chr1:179220648-179221414	SK-N-SH	brain:	n/a	n/a
7	FOXA1	chr1:179220878-179221228	T-47D	breast:	n/a	n/a
8	SMC3	chr1:179220872-179221195	K562	blood:	n/a	n/a
9	RAD21	chr1:179220847-179221273	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr1:179220806-179221184	K562	blood:	n/a	n/a
11	CTCF	chr1:179220832-179221231	K562	blood:	n/a	n/a
12	CTCF	chr1:179220665-179221385	A549	lung:	n/a	n/a
13	SMC3	chr1:179220842-179221259	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr1:179220792-179221234	HepG2	liver:	n/a	n/a
15	CTCF	chr1:179220795-179221293	A549	lung:	n/a	n/a
16	CTCF	chr1:179220567-179221436	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr1:179220729-179221311	HepG2	liver:	n/a	n/a
18	RAD21	chr1:179220781-179221302	ECC-1	luminal epithelium:	n/a	n/a
19	RAD21	chr1:179220796-179221414	HCT-116	colon:	n/a	n/a
20	RAD21	chr1:179220863-179221223	SK-N-SH_RA	brain:	n/a	n/a
21	STAT3	chr1:179220877-179221087	MCF10A-Er-Src	breast:	n/a	chr1:179221001-179221010 chr1:179221000-179221009 chr1:179220999-179221010
22	RAD21	chr1:179220745-179221352	MCF-7	breast:	n/a	n/a
23	CTCF	chr1:179220726-179221273	HCT-116	colon:	n/a	n/a
24	RFX5	chr1:179220840-179221205	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:179220878-179221180	K562	blood:	n/a	n/a
26	RAD21	chr1:179220804-179221269	Hela-S3	cervix:	n/a	n/a
27	RAD21	chr1:179220817-179221264	SK-N-SH_RA	brain:	n/a	n/a
28	RAD21	chr1:179220877-179221233	GM12878	blood:	n/a	n/a
29	SMC3	chr1:179220869-179221212	GM12878	blood:	n/a	n/a
30	RAD21	chr1:179220762-179221339	A549	lung:	n/a	n/a
31	RAD21	chr1:179220786-179221380	MCF-7	breast:	n/a	n/a
32	CTCF	chr1:179220852-179221181	A549	lung:	n/a	n/a
33	RAD21	chr1:179220852-179221241	IMR90	lung:	n/a	n/a
34	CTCF	chr1:179220860-179221010	GM12870	blood:	n/a	n/a
35	CTCF	chr1:179220860-179221010	A549	lung:	n/a	n/a
36	CTCF	chr1:179220769-179221334	MCF-7	breast:	n/a	n/a
37	CTCF	chr1:179220746-179221294	HCT-116	colon:	n/a	n/a
38	RAD21	chr1:179220789-179221286	A549	lung:	n/a	n/a
39	SMC3	chr1:179220711-179221419	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr1:179220872-179221256	T-47D	breast:	n/a	n/a
41	RAD21	chr1:179220737-179221297	HCT-116	colon:	n/a	n/a
42	CTCF	chr1:179220829-179221211	IMR90	lung:	n/a	n/a
43	RAD21	chr1:179220842-179221257	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:179090099..179090850-chr1:179220628..179221510,2	MCF-7	breast:
2	chr1:179220558..179221464-chr1:179338599..179339569,5	MCF-7	breast:
3	chr1:179220618..179221536-chr1:179778672..179779568,2	MCF-7	breast:
4	chr1:179220379..179221592-chr1:179260995..179261928,6	MCF-7	breast:
5	chr1:179220394..179221467-chr1:179338651..179339953,9	MCF-7	breast:
6	chr1:179220599..179221512-chr1:179261221..179261896,5	MCF-7	breast:

No data

Variant related genes	Relation type
COX5BP8	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1046385	0.85[JPT][hapmap]
rs1078872	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs10798652	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs10913690	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10913695	0.88[EUR][1000 genomes]
rs10913697	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs12080991	0.83[YRI][hapmap]
rs12130276	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs12239073	0.82[AFR][1000 genomes]
rs1325194	0.81[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap]
rs1325195	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs17362081	0.80[JPT][hapmap]
rs1856967	0.89[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1858551	0.88[EUR][1000 genomes]
rs2066279	1.00[CEU][hapmap];0.83[JPT][hapmap];0.97[EUR][1000 genomes]
rs2087559	0.92[EUR][1000 genomes]
rs2130576	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs2171959	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2258217	0.90[EUR][1000 genomes]
rs2258221	0.87[EUR][1000 genomes]
rs2486995	0.88[EUR][1000 genomes]
rs2486997	0.88[EUR][1000 genomes]
rs2493124	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2636265	0.97[EUR][1000 genomes]
rs2636266	0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs2636274	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2636276	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2636280	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2636281	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636282	0.98[EUR][1000 genomes]
rs2636287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2636290	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs2791940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2791943	0.89[EUR][1000 genomes]
rs2793793	0.92[EUR][1000 genomes]
rs2793795	0.82[EUR][1000 genomes]
rs2793796	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs2793797	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2793798	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs2793799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793803	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs2793805	0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs2793806	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2793812	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2793816	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap]
rs2816167	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816183	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs2816185	0.89[EUR][1000 genomes]
rs2816186	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2816187	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs2816189	0.91[EUR][1000 genomes]
rs2816196	0.89[EUR][1000 genomes]
rs2816197	0.92[EUR][1000 genomes]
rs2816198	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs2816199	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs2816201	0.82[JPT][hapmap]
rs2816202	0.93[EUR][1000 genomes]
rs2816203	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2816204	0.93[EUR][1000 genomes]
rs2816206	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816208	0.97[EUR][1000 genomes]
rs2816209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816210	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2816211	0.98[EUR][1000 genomes]
rs2816213	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap]
rs2816214	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes]
rs3210839	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs36122838	0.86[EUR][1000 genomes]
rs377785	0.99[EUR][1000 genomes]
rs3813642	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs3813643	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs3818433	0.95[GIH][hapmap];0.80[TSI][hapmap]
rs411266	1.00[CEU][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes]
rs434283	0.99[EUR][1000 genomes]
rs451088	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs4651012	0.86[EUR][1000 genomes]
rs4651013	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs4651014	0.81[JPT][hapmap]
rs915337	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs931441	0.81[JPT][hapmap]
rs9650996	0.81[YRI][hapmap]
rs965401	0.91[EUR][1000 genomes]
rs9726961	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs9727252	0.88[EUR][1000 genomes]
rs9728480	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs9729199	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179218600-179225600	Weak transcription	Spleen	Spleen

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