Variant report

Variant	rs7959703
Chromosome Location	chr12:41084497-41084498
allele	A/C
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	STAT3	chr12:41084138-41084557	MCF10A-Er-Src	breast:	n/a	n/a
2	SP1	chr12:41084197-41084574	HCT-116	colon:	n/a	n/a
3	SP1	chr12:41084208-41084545	A549	lung:	n/a	n/a
4	JUND	chr12:41084274-41084569	A549	lung:	n/a	n/a
5	GABPA	chr12:41084195-41084531	A549	lung:	n/a	n/a
6	REST	chr12:41084121-41084560	ECC-1	luminal epithelium:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
7	CEBPB	chr12:41084268-41084524	HepG2	liver:	n/a	n/a
8	CEBPB	chr12:41084053-41084569	A549	lung:	n/a	n/a
9	REST	chr12:41084204-41084545	MCF-7	breast:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
10	REST	chr12:41084232-41084544	HCT-116	colon:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
11	JUND	chr12:41084265-41084551	HCT-116	colon:	n/a	n/a
12	STAT3	chr12:41084236-41084579	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr12:41084203-41084776	A549	lung:	n/a	n/a
14	REST	chr12:41084039-41084542	A549	lung:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
15	FOS	chr12:41084221-41084610	MCF10A-Er-Src	breast:	n/a	n/a
16	FOSL1	chr12:41084181-41084592	HCT-116	colon:	n/a	n/a
17	CEBPB	chr12:41084168-41084583	A549	lung:	n/a	n/a
18	CEBPB	chr12:41084041-41084590	HCT-116	colon:	n/a	n/a
19	E2F4	chr12:41084276-41084500	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr12:41084209-41084583	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr12:41084151-41084563	ECC-1	luminal epithelium:	n/a	n/a
22	FOSL1	chr12:41084156-41084571	HCT-116	colon:	n/a	n/a
23	FOS	chr12:41084203-41084596	MCF10A-Er-Src	breast:	n/a	n/a
24	SP1	chr12:41084103-41084654	A549	lung:	n/a	n/a
25	REST	chr12:41084172-41084566	MCF-7	breast:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
26	REST	chr12:41084152-41084553	HCT-116	colon:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
27	CEBPB	chr12:41084159-41084588	HCT-116	colon:	n/a	n/a
28	FOSL2	chr12:41084211-41084536	A549	lung:	n/a	n/a
29	REST	chr12:41084149-41084541	A549	lung:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
30	FOS	chr12:41084194-41084597	MCF10A-Er-Src	breast:	n/a	n/a
31	REST	chr12:41084138-41084552	ECC-1	luminal epithelium:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
32	STAT3	chr12:41084246-41084551	MCF10A-Er-Src	breast:	n/a	n/a
33	CEBPB	chr12:41084252-41084501	MCF-7	breast:	n/a	n/a
34	CEBPB	chr12:41084232-41084531	ECC-1	luminal epithelium:	n/a	n/a
35	FOSL2	chr12:41084026-41084645	A549	lung:	n/a	n/a
36	FOS	chr12:41084157-41084611	MCF10A-Er-Src	breast:	n/a	n/a
37	REST	chr12:41084167-41084535	Hela-S3	cervix:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
38	STAT3	chr12:41084247-41084572	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr12:41084264-41084540	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CNTN1	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10506173	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784813	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348509	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373424	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444204	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584093	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596509	0.90[EUR][1000 genomes]
rs17128385	1.00[ASN][1000 genomes]
rs17128536	1.00[ASN][1000 genomes]
rs17128689	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1816856	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867430	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992607	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2053629	0.89[EUR][1000 genomes]
rs2120599	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405018	1.00[ASN][1000 genomes]
rs4275691	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55635729	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736346	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55775102	1.00[ASN][1000 genomes]
rs55786396	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56032335	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56245194	1.00[ASN][1000 genomes]
rs56322620	1.00[ASN][1000 genomes]
rs56334222	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56383533	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57772297	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57816451	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59066229	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581906	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581931	0.90[EUR][1000 genomes]
rs6581934	0.90[EUR][1000 genomes]
rs7137967	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138084	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296616	0.89[EUR][1000 genomes]
rs73110067	1.00[ASN][1000 genomes]
rs73110075	1.00[ASN][1000 genomes]
rs73110852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110883	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73115378	1.00[ASN][1000 genomes]
rs73115394	1.00[ASN][1000 genomes]
rs73115401	1.00[ASN][1000 genomes]
rs73117512	1.00[ASN][1000 genomes]
rs73119913	1.00[ASN][1000 genomes]
rs73123118	1.00[ASN][1000 genomes]
rs73123119	1.00[ASN][1000 genomes]
rs73123140	1.00[ASN][1000 genomes]
rs7314530	1.00[ASN][1000 genomes]
rs74076704	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076712	0.95[EUR][1000 genomes]
rs74078532	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078558	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078563	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078569	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078570	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484715	1.00[ASN][1000 genomes]
rs7977934	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935230	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv832378	chr12:40943111-41132305	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2751098	chr12:41082399-41180235	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41081000-41085800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:41082200-41085600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:41082400-41085800	Weak transcription	Ovary	ovary
4	chr12:41083000-41085600	Enhancers	NHEK	skin
5	chr12:41083200-41085600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:41083800-41086000	Enhancers	HMEC	breast
7	chr12:41084000-41085000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:41084000-41085000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:41084400-41084800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:41084400-41085000	Active TSS	A549	lung

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