Variant report

Variant	rs7972371
Chromosome Location	chr12:41084445-41084446
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	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	REST	chr12:41084222-41084478	Hela-S3	cervix:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
4	SP1	chr12:41084208-41084545	A549	lung:	n/a	n/a
5	JUND	chr12:41084274-41084569	A549	lung:	n/a	n/a
6	GABPA	chr12:41084195-41084531	A549	lung:	n/a	n/a
7	REST	chr12:41084121-41084560	ECC-1	luminal epithelium:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
8	CEBPB	chr12:41084268-41084524	HepG2	liver:	n/a	n/a
9	CEBPB	chr12:41084053-41084569	A549	lung:	n/a	n/a
10	REST	chr12:41084204-41084545	MCF-7	breast:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
11	REST	chr12:41084232-41084544	HCT-116	colon:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
12	JUND	chr12:41084265-41084551	HCT-116	colon:	n/a	n/a
13	STAT3	chr12:41084236-41084579	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr12:41084203-41084776	A549	lung:	n/a	n/a
15	MYC	chr12:41084203-41084493	MCF10A-Er-Src	breast:	n/a	n/a
16	REST	chr12:41084039-41084542	A549	lung:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
17	FOS	chr12:41084221-41084610	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL1	chr12:41084181-41084592	HCT-116	colon:	n/a	n/a
19	CEBPB	chr12:41084168-41084583	A549	lung:	n/a	n/a
20	CEBPB	chr12:41084041-41084590	HCT-116	colon:	n/a	n/a
21	E2F4	chr12:41084276-41084500	MCF10A-Er-Src	breast:	n/a	n/a
22	CEBPB	chr12:41084209-41084583	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr12:41084151-41084563	ECC-1	luminal epithelium:	n/a	n/a
24	FOSL1	chr12:41084156-41084571	HCT-116	colon:	n/a	n/a
25	FOS	chr12:41084203-41084596	MCF10A-Er-Src	breast:	n/a	n/a
26	SP1	chr12:41084103-41084654	A549	lung:	n/a	n/a
27	REST	chr12:41084172-41084566	MCF-7	breast:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
28	REST	chr12:41084152-41084553	HCT-116	colon:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
29	CEBPB	chr12:41084159-41084588	HCT-116	colon:	n/a	n/a
30	FOSL2	chr12:41084211-41084536	A549	lung:	n/a	n/a
31	REST	chr12:41084149-41084541	A549	lung:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
32	FOS	chr12:41084194-41084597	MCF10A-Er-Src	breast:	n/a	n/a
33	REST	chr12:41084138-41084552	ECC-1	luminal epithelium:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
34	STAT3	chr12:41084246-41084551	MCF10A-Er-Src	breast:	n/a	n/a
35	CEBPB	chr12:41084252-41084501	MCF-7	breast:	n/a	n/a
36	CEBPB	chr12:41084232-41084531	ECC-1	luminal epithelium:	n/a	n/a
37	FOSL2	chr12:41084026-41084645	A549	lung:	n/a	n/a
38	FOS	chr12:41084157-41084611	MCF10A-Er-Src	breast:	n/a	n/a
39	REST	chr12:41084167-41084535	Hela-S3	cervix:	n/a	chr12:41084366-41084386 chr12:41084366-41084386
40	CEBPB	chr12:41084425-41084448	K562	blood:	n/a	n/a
41	STAT3	chr12:41084247-41084572	MCF10A-Er-Src	breast:	n/a	n/a
42	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: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013929	0.88[ASN][1000 genomes]
rs10161138	0.93[ASN][1000 genomes]
rs10735957	0.88[ASN][1000 genomes]
rs10748138	0.91[ASN][1000 genomes]
rs10748142	0.96[ASN][1000 genomes]
rs10748148	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10784796	0.88[ASN][1000 genomes]
rs10784797	0.85[ASN][1000 genomes]
rs10784800	0.88[ASN][1000 genomes]
rs10879019	0.83[ASN][1000 genomes]
rs10879028	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879031	0.84[ASN][1000 genomes]
rs10879079	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879092	0.86[ASN][1000 genomes]
rs10879095	0.83[ASN][1000 genomes]
rs10879131	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11177809	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11177862	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11177863	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11177886	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11177927	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11177961	0.80[ASN][1000 genomes]
rs11178000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178013	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178015	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178017	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178018	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178027	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178050	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11178067	0.86[ASN][1000 genomes]
rs11178070	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178118	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11178122	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12367287	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367708	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12372385	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373425	0.88[ASN][1000 genomes]
rs1373426	0.88[ASN][1000 genomes]
rs1584090	0.83[ASN][1000 genomes]
rs1584094	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1584095	0.88[ASN][1000 genomes]
rs1584100	0.83[ASN][1000 genomes]
rs1596538	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1816855	0.96[ASN][1000 genomes]
rs1899829	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1992606	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405293	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405294	0.88[ASN][1000 genomes]
rs2405295	0.96[ASN][1000 genomes]
rs3940638	0.87[ASN][1000 genomes]
rs61915074	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61915099	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915100	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915101	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915102	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581905	0.99[ASN][1000 genomes]
rs7133642	0.86[ASN][1000 genomes]
rs7139243	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311914	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7312935	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73267740	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7953546	0.88[ASN][1000 genomes]
rs7960217	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961129	0.91[ASN][1000 genomes]
rs7962501	0.88[ASN][1000 genomes]
rs7967298	0.99[ASN][1000 genomes]
rs7971056	0.96[ASN][1000 genomes]
rs7974939	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935224	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9669757	0.90[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs9783468	0.86[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7972371	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx
rs7972371	CNTN1	cis	normal skin	skin_eQTL

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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