Variant report

Variant	rs10160886
Chromosome Location	chr12:85549891-85549892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:85549548-85549900	A549	lung:	n/a	n/a
2	CTCF	chr12:85549443-85549980	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr12:85549530-85550019	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr12:85549466-85550112	A549	lung:	n/a	n/a
5	MYC	chr12:85549633-85550015	MCF10A-Er-Src	breast:	n/a	n/a
6	RAD21	chr12:85549532-85549917	ECC-1	luminal epithelium:	n/a	n/a
7	RAD21	chr12:85549516-85550032	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr12:85549453-85550018	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr12:85549352-85550081	A549	lung:	n/a	n/a
10	RAD21	chr12:85549496-85549993	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr12:85549605-85549921	A549	lung:	n/a	n/a
12	CTCF	chr12:85549597-85549985	MCF-7	breast:	n/a	n/a
13	CTCF	chr12:85549800-85549950	NHEK	skin:	n/a	n/a
14	RAD21	chr12:85549542-85549962	SK-N-SH_RA	brain:	n/a	n/a
15	RAD21	chr12:85549541-85549967	HepG2	liver:	n/a	n/a
16	RAD21	chr12:85549283-85550035	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr12:85549595-85549987	HCT-116	colon:	n/a	n/a
18	GATA3	chr12:85549495-85549938	SH-SY5Y	brain:	n/a	n/a
19	RAD21	chr12:85549548-85549990	MCF-7	breast:	n/a	n/a
20	CTCF	chr12:85549760-85549910	HEK293	kidney:	n/a	n/a
21	RAD21	chr12:85549504-85550104	HCT-116	colon:	n/a	n/a
22	RAD21	chr12:85549461-85550035	HCT-116	colon:	n/a	n/a
23	SMC3	chr12:85549491-85550023	Hela-S3	cervix:	n/a	chr12:85549757-85549771
24	CTCF	chr12:85549780-85549930	A549	lung:	n/a	n/a
25	CTCF	chr12:85549623-85549912	HUVEC	blood vessel:	n/a	n/a
26	CTCF	chr12:85549585-85549932	GM12878	blood:	n/a	n/a
27	CTCF	chr12:85549780-85549930	BE2_C	brain:	n/a	n/a
28	GATA3	chr12:85549508-85549978	MCF-7	breast:	n/a	n/a
29	RAD21	chr12:85549585-85549952	H1-hESC	embryonic stem cell:	n/a	n/a
30	SMC3	chr12:85549329-85549902	SK-N-SH	brain:	n/a	chr12:85549757-85549771
31	CTCF	chr12:85549485-85550006	HCT-116	colon:	n/a	n/a
32	RAD21	chr12:85549565-85550027	SK-N-SH_RA	brain:	n/a	n/a
33	RAD21	chr12:85549531-85549991	MCF-7	breast:	n/a	n/a
34	E2F4	chr12:85549704-85549904	MCF10A-Er-Src	breast:	n/a	n/a
35	CTCF	chr12:85549513-85549969	A549	lung:	n/a	n/a
36	CTCF	chr12:85549587-85549919	H1-hESC	embryonic stem cell:	n/a	n/a
37	GATA3	chr12:85549614-85549940	T-47D	breast:	n/a	n/a
38	RAD21	chr12:85549548-85550061	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:85549075..85550214-chr12:85841829..85842800,6	MCF-7	breast:
2	chr12:85549530..85550247-chr12:86266080..86266618,2	MCF-7	breast:
3	chr12:85549387..85549978-chr12:85835659..85836204,2	MCF-7	breast:

No data

Variant related genes	Relation type
LRRIQ1	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10506911	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10506912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap]
rs10779148	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10862955	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11116701	0.95[CEU][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11116702	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs11116704	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11116707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap]
rs11116708	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs11116712	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11532387	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11608487	0.86[CEU][hapmap]
rs11609088	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs11612309	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs12227853	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12227986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12229124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12229923	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12231122	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs12301980	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12810608	0.82[GIH][hapmap]
rs12814669	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs12817187	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823090	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1389798	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap]
rs1404867	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404868	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1494500	0.91[ASN][1000 genomes]
rs1507214	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1525548	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17012522	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17012533	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs17012616	0.86[ASN][1000 genomes]
rs1838671	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1973816	0.91[ASN][1000 genomes]
rs1976270	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2048123	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2174754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305102	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2404773	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765044	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4074726	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs4761074	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4761075	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4761077	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap]
rs4761113	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4761114	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4761115	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4761123	0.97[EUR][1000 genomes]
rs66617212	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7133493	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135053	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap]
rs718553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7302315	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs7304576	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7954110	0.91[ASN][1000 genomes]
rs7956568	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs7962411	0.91[ASN][1000 genomes]
rs7965562	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7966105	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7974623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7976514	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899377	chr12:85157346-85629241	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv899387	chr12:85427691-85629241	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv455669	chr12:85427691-85638089	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv559653	chr12:85427691-85638089	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv899388	chr12:85427691-85766847	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv455670	chr12:85465932-85603531	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv559654	chr12:85465932-85603531	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1052676	chr12:85466799-85556788	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1040622	chr12:85502226-85693132	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv541558	chr12:85502226-85693132	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv455671	chr12:85519246-85566208	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv559656	chr12:85519246-85566208	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv899391	chr12:85519246-85576492	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv455672	chr12:85522932-85566208	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv559657	chr12:85522932-85566208	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv455673	chr12:85522932-85603531	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv455674	chr12:85522932-85603531	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv559658	chr12:85522932-85603531	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv559659	chr12:85524140-85575028	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv455676	chr12:85529349-85603531	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv455677	chr12:85529349-85603531	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv559660	chr12:85529349-85603531	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv559661	chr12:85544429-85638089	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv559662	chr12:85544429-85734069	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85547800-85550000	Active TSS	Fetal Kidney	kidney
2	chr12:85549800-85550400	Enhancers	Hela-S3	cervix

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