Variant report

Variant	rs1538460
Chromosome Location	chr6:113975908-113975909
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	TCF12	chr6:113975508-113976048	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr6:113975513-113976153	A549	lung:	n/a	n/a
3	POLR2A	chr6:113975590-113976046	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr6:113975558-113976156	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr6:113975535-113976045	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr6:113975421-113976194	ECC-1	luminal epithelium:	n/a	n/a
7	E2F4	chr6:113975342-113976171	MCF10A-Er-Src	breast:	n/a	n/a
8	RCOR1	chr6:113975660-113975979	Hela-S3	cervix:	n/a	n/a
9	EP300	chr6:113975593-113976065	A549	lung:	n/a	n/a
10	MAX	chr6:113975630-113975982	Hela-S3	cervix:	n/a	chr6:113975820-113975829
11	NFIC	chr6:113975479-113976145	ECC-1	luminal epithelium:	n/a	n/a
12	STAT3	chr6:113975557-113976860	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr6:113975500-113976208	MCF10A-Er-Src	breast:	n/a	n/a
14	PBX3	chr6:113975540-113976080	SK-N-SH	brain:	n/a	n/a
15	MAX	chr6:113975575-113976055	SK-N-SH	brain:	n/a	chr6:113975820-113975829
16	POLR2A	chr6:113975566-113975971	U87	brain:	n/a	n/a
17	EP300	chr6:113975680-113975994	SK-N-SH_RA	brain:	n/a	n/a
18	EP300	chr6:113975654-113976150	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:113975598-113975971	U87	brain:	n/a	n/a
20	GATA3	chr6:113975425-113976298	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr6:113975655-113976078	ECC-1	luminal epithelium:	n/a	n/a
22	JUND	chr6:113975609-113975974	A549	lung:	n/a	chr6:113975821-113975829
23	SP1	chr6:113975581-113976175	HCT-116	colon:	n/a	chr6:113975688-113975709
24	GATA3	chr6:113975419-113976239	SK-N-SH	brain:	n/a	n/a
25	STAT3	chr6:113975587-113976284	MCF10A-Er-Src	breast:	n/a	n/a
26	TCF12	chr6:113975442-113976241	SK-N-SH	brain:	n/a	n/a
27	FOSL2	chr6:113975576-113976122	A549	lung:	n/a	chr6:113975821-113975829
28	CEBPB	chr6:113975649-113976062	MCF-7	breast:	n/a	n/a
29	FOS	chr6:113975508-113976315	MCF10A-Er-Src	breast:	n/a	chr6:113975821-113975829
30	FOS	chr6:113975550-113976135	MCF10A-Er-Src	breast:	n/a	chr6:113975821-113975829
31	RFX5	chr6:113975575-113975966	Hela-S3	cervix:	n/a	n/a
32	STAT3	chr6:113975407-113976363	MCF10A-Er-Src	breast:	n/a	n/a
33	GATA3	chr6:113975539-113976098	A549	lung:	n/a	n/a
34	STAT3	chr6:113975170-113976535	MCF10A-Er-Src	breast:	n/a	chr6:113975211-113975222
35	CEBPB	chr6:113975585-113976075	HCT-116	colon:	n/a	n/a
36	MYC	chr6:113975424-113976223	MCF10A-Er-Src	breast:	n/a	chr6:113975820-113975829
37	SP1	chr6:113975605-113976079	A549	lung:	n/a	chr6:113975688-113975709
38	SMC3	chr6:113975622-113976015	Hela-S3	cervix:	n/a	n/a
39	TEAD4	chr6:113975573-113976180	SK-N-SH	brain:	n/a	n/a
40	REST	chr6:113975718-113975911	Hela-S3	cervix:	n/a	n/a
41	TBP	chr6:113975632-113976018	Hela-S3	cervix:	n/a	n/a
42	TCF12	chr6:113975445-113976341	SK-N-SH	brain:	n/a	n/a
43	CBX3	chr6:113975496-113976124	HCT-116	colon:	n/a	chr6:113975545-113975556
44	POLR2A	chr6:113974954-113976316	MCF10A-Er-Src	breast:	n/a	n/a
45	EP300	chr6:113975577-113976126	A549	lung:	n/a	n/a
46	CEBPB	chr6:113975605-113976009	A549	lung:	n/a	n/a
47	YY1	chr6:113975626-113975942	HCT-116	colon:	n/a	n/a
48	CEBPB	chr6:113975596-113976036	Hela-S3	cervix:	n/a	n/a
49	NFIC	chr6:113975391-113976395	SK-N-SH	brain:	n/a	n/a
50	TCF12	chr6:113975484-113976177	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:113975747..113977411-chr6:114176433..114178973,2	MCF-7	breast:
2	chr6:113951494..113953061-chr6:113975155..113977027,2	MCF-7	breast:
3	chr6:113973673..113976294-chr6:114178537..114180180,2	MCF-7	breast:
4	chr20:46442704..46445148-chr6:113974663..113976221,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230943	TF binding region
ENSG00000155130	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10732719	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11153426	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339040	0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339041	1.00[AMR][1000 genomes]
rs1383805	0.83[AMR][1000 genomes]
rs1481433	0.83[AMR][1000 genomes]
rs2003888	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2127989	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4632923	1.00[AMR][1000 genomes]
rs4945500	0.83[AMR][1000 genomes]
rs4945960	0.83[AMR][1000 genomes]
rs4945961	0.83[AMR][1000 genomes]
rs4945962	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6911610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6917191	1.00[AMR][1000 genomes]
rs6925360	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6930982	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6940419	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs922722	1.00[AMR][1000 genomes]
rs9320466	0.83[AMR][1000 genomes]
rs9374409	0.83[AMR][1000 genomes]
rs9374413	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9374414	0.86[AFR][1000 genomes]
rs9384877	0.86[AFR][1000 genomes]
rs9387158	0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9387163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9400646	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9400647	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9400648	0.83[AMR][1000 genomes]
rs9400655	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1538460	MARCKS	cis	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113967600-113980600	Weak transcription	Placenta	Placenta
2	chr6:113970800-113977400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:113971200-113976000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:113971400-113981000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:113971600-113979000	Weak transcription	HepG2	liver
6	chr6:113972600-113976000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:113974800-113976200	Enhancers	Liver	Liver
8	chr6:113974800-113976200	Enhancers	HMEC	breast
9	chr6:113974800-113977600	Enhancers	NHEK	skin
10	chr6:113975000-113976200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:113975000-113976200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:113975000-113976600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:113975000-113982000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:113975200-113976000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:113975200-113976000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:113975200-113976000	Enhancers	GM12878-XiMat	blood
17	chr6:113975200-113976400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:113975200-113976600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:113975400-113976200	Enhancers	Stomach Mucosa	stomach
20	chr6:113975400-113976600	Enhancers	HUVEC	blood vessel
21	chr6:113975400-113976600	Enhancers	Osteobl	bone
22	chr6:113975400-113981200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:113975600-113976000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:113975600-113976000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:113975600-113976000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:113975600-113976000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:113975600-113976000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:113975600-113976000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:113975600-113976000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:113975600-113976000	Enhancers	Brain Hippocampus Middle	brain
31	chr6:113975600-113976000	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr6:113975600-113976000	Enhancers	Fetal Muscle Leg	muscle
33	chr6:113975600-113976000	Enhancers	Gastric	stomach
34	chr6:113975600-113976000	Enhancers	Psoas Muscle	Psoas
35	chr6:113975600-113976000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:113975600-113976000	Enhancers	HSMMtube	muscle
37	chr6:113975600-113976200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:113975600-113976200	Enhancers	NHDF-Ad	bronchial
39	chr6:113975600-113976400	Enhancers	Hela-S3	cervix
40	chr6:113975600-113976400	Enhancers	NH-A	brain
41	chr6:113975600-113977600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:113975800-113976000	Enhancers	Aorta	Aorta
43	chr6:113975800-113976000	Flanking Active TSS	A549	lung

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