Variant report

Variant	rs11178982
Chromosome Location	chr12:41301332-41301333
allele	C/T
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	CEBPB	chr12:41300754-41301591	A549	lung:	n/a	n/a
2	SP1	chr12:41300630-41301606	HCT-116	colon:	n/a	n/a
3	FOS	chr12:41300864-41301387	MCF10A-Er-Src	breast:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
4	FOSL2	chr12:41300773-41301499	A549	lung:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
5	FOS	chr12:41300783-41301426	MCF10A-Er-Src	breast:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
6	MAX	chr12:41300818-41301585	HCT-116	colon:	n/a	n/a
7	MAX	chr12:41300882-41301431	Hela-S3	cervix:	n/a	n/a
8	NFIC	chr12:41300708-41301505	GM12878	blood:	n/a	n/a
9	FOSL1	chr12:41300609-41301566	HCT-116	colon:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
10	EBF1	chr12:41300893-41301361	GM12878	blood:	n/a	n/a
11	CEBPB	chr12:41300709-41301627	HCT-116	colon:	n/a	n/a
12	NFIC	chr12:41300711-41301397	GM12878	blood:	n/a	n/a
13	JUND	chr12:41300630-41301469	HCT-116	colon:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
14	ATF3	chr12:41300763-41301489	HCT-116	colon:	n/a	n/a
15	PAX5	chr12:41301007-41301340	GM12878	blood:	n/a	n/a
16	CEBPB	chr12:41301195-41301363	HepG2	liver:	n/a	n/a
17	CEBPB	chr12:41300760-41301507	Hela-S3	cervix:	n/a	n/a
18	CBX3	chr12:41300680-41301419	HCT-116	colon:	n/a	n/a
19	PAX5	chr12:41300954-41301501	GM12891	blood:	n/a	n/a
20	MYC	chr12:41300962-41301411	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr12:41300797-41301432	MCF10A-Er-Src	breast:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
22	JUND	chr12:41300652-41301539	HCT-116	colon:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
23	PAX5	chr12:41301061-41301367	GM12878	blood:	n/a	n/a
24	SP1	chr12:41300619-41301541	HCT-116	colon:	n/a	n/a
25	BATF	chr12:41300829-41301349	GM12878	blood:	n/a	n/a
26	CEBPB	chr12:41300659-41301721	HCT-116	colon:	n/a	n/a
27	CBX3	chr12:41300743-41301398	HCT-116	colon:	n/a	n/a
28	MEF2A	chr12:41300834-41301434	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:41300959-41301390	HCT-116	colon:	n/a	n/a
30	CEBPB	chr12:41300876-41301443	A549	lung:	n/a	n/a
31	MAX	chr12:41300679-41301497	HCT-116	colon:	n/a	n/a
32	RUNX3	chr12:41300719-41301482	GM12878	blood:	n/a	n/a
33	FOS	chr12:41300783-41301425	MCF10A-Er-Src	breast:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
34	FOSL1	chr12:41300696-41301497	HCT-116	colon:	n/a	chr12:41300985-41300993 chr12:41300985-41300992
35	USF2	chr12:41300879-41301435	Hela-S3	cervix:	n/a	chr12:41301342-41301353
36	TEAD4	chr12:41300703-41301502	HCT-116	colon:	n/a	n/a
37	ATF3	chr12:41300812-41301420	HCT-116	colon:	n/a	n/a
38	EP300	chr12:41300834-41301448	Hela-S3	cervix:	n/a	chr12:41300895-41300902
39	TCF12	chr12:41300733-41301570	A549	lung:	n/a	n/a
40	RUNX3	chr12:41300755-41301411	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CNTN1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10879356	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879360	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11178979	0.85[CEU][hapmap];0.93[YRI][hapmap]
rs11179040	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11179042	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1442187	0.82[EUR][1000 genomes]
rs17621741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2772458	0.82[EUR][1000 genomes]
rs312269	0.82[EUR][1000 genomes]
rs312273	0.82[EUR][1000 genomes]
rs3816251	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768319	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs56294359	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7139018	0.80[YRI][hapmap]
rs7970381	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11178982	GXYLT1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41285000-41304600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:41297200-41338600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:41297400-41328600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:41297400-41338600	Weak transcription	Brain Angular Gyrus	brain
5	chr12:41297400-41346400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:41300400-41301400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:41300400-41302200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:41300400-41302200	Enhancers	NHEK	skin
9	chr12:41300600-41302000	Enhancers	HMEC	breast
10	chr12:41300600-41302200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:41300800-41301400	Flanking Active TSS	A549	lung
12	chr12:41300800-41301600	Enhancers	GM12878-XiMat	blood
13	chr12:41301000-41301400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr12:41301000-41301400	Enhancers	Hela-S3	cervix
15	chr12:41301200-41316000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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