Variant report

Variant	rs2660449
Chromosome Location	chr12:85549810-85549811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:85549720-85549870	HepG2	liver:	n/a	n/a
2	GATA2	chr12:85549536-85549887	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr12:85549548-85549900	A549	lung:	n/a	n/a
4	CTCF	chr12:85549443-85549980	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr12:85549530-85550019	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr12:85549636-85549890	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr12:85549660-85549810	NB4	blood:	n/a	n/a
8	CTCF	chr12:85549740-85549890	HMF	breast:	n/a	n/a
9	CTCF	chr12:85549660-85549810	AG04450	lung:	n/a	n/a
10	CTCF	chr12:85549660-85549810	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr12:85549680-85549830	HPAF	blood vessel:	n/a	n/a
12	RAD21	chr12:85549466-85550112	A549	lung:	n/a	n/a
13	CTCF	chr12:85549720-85549870	HPF	lung:	n/a	n/a
14	MYC	chr12:85549633-85550015	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr12:85549680-85549830	HEEpiC	esophagus:	n/a	n/a
16	CTCF	chr12:85549685-85549819	GM13977	blood:	n/a	n/a
17	RAD21	chr12:85549532-85549917	ECC-1	luminal epithelium:	n/a	n/a
18	RAD21	chr12:85549516-85550032	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr12:85549664-85549839	LNCaP	prostate:	n/a	n/a
20	GATA3	chr12:85549453-85550018	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr12:85549352-85550081	A549	lung:	n/a	n/a
22	CTCF	chr12:85549660-85549810	WERI-Rb-1	eye:	n/a	n/a
23	CTCF	chr12:85549675-85549845	LNCaP	prostate:	n/a	n/a
24	CTCF	chr12:85549680-85549830	AG10803	skin:	n/a	n/a
25	RAD21	chr12:85549496-85549993	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr12:85549605-85549921	A549	lung:	n/a	n/a
27	CTCF	chr12:85549597-85549985	MCF-7	breast:	n/a	n/a
28	CTCF	chr12:85549800-85549950	NHEK	skin:	n/a	n/a
29	CTCF	chr12:85549700-85549850	HPF	lung:	n/a	n/a
30	CTCF	chr12:85549630-85549856	SK-N-SH_RA	brain:	n/a	n/a
31	CTCF	chr12:85549720-85549870	HCPEpiC	choroid plexus:	n/a	n/a
32	RAD21	chr12:85549542-85549962	SK-N-SH_RA	brain:	n/a	n/a
33	RAD21	chr12:85549541-85549967	HepG2	liver:	n/a	n/a
34	CTCF	chr12:85549702-85549813	MCF-7	breast:	n/a	n/a
35	CTCF	chr12:85549714-85549823	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:85549776-85549826	MCF10A-Er-Src	breast:	n/a	n/a
37	RAD21	chr12:85549283-85550035	SK-N-SH	brain:	n/a	n/a
38	CTCF	chr12:85549595-85549987	HCT-116	colon:	n/a	n/a
39	CTCF	chr12:85549720-85549870	HPAF	blood vessel:	n/a	n/a
40	GATA3	chr12:85549495-85549938	SH-SY5Y	brain:	n/a	n/a
41	RAD21	chr12:85549548-85549990	MCF-7	breast:	n/a	n/a
42	RAD21	chr12:85549579-85549884	ECC-1	luminal epithelium:	n/a	n/a
43	CTCF	chr12:85549720-85549870	HFF-Myc	foreskin:	n/a	n/a
44	CTCF	chr12:85549630-85549881	Medullo	brain:	n/a	n/a
45	CTCF	chr12:85549680-85549830	AG04449	skin:	n/a	n/a
46	CTCF	chr12:85549662-85549868	A549	lung:	n/a	n/a
47	RAD21	chr12:85549643-85549830	GM12878	blood:	n/a	n/a
48	CTCF	chr12:85549760-85549910	HEK293	kidney:	n/a	n/a
49	CTCF	chr12:85549700-85549850	BJ	skin:	n/a	n/a
50	CTCF	chr12:85549700-85549850	HRPEpiC	eye:	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: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1031190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11116694	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12301980	0.85[EUR][1000 genomes]
rs12304556	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12810608	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1494500	0.85[EUR][1000 genomes]
rs1494501	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507209	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1512732	0.86[CHB][hapmap]
rs1525548	0.85[EUR][1000 genomes]
rs168613	0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs168615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690835	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1852148	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1973816	0.85[EUR][1000 genomes]
rs2056638	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2660454	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2660455	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2660459	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708496	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708498	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs359992	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6539879	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6539881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132596	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7133817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302312	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316900	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7486483	0.86[CHB][hapmap]
rs777035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7954110	0.85[EUR][1000 genomes]
rs7962411	0.85[EUR][1000 genomes]
rs7962577	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs796567	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7974418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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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