Variant report

Variant	rs6663545
Chromosome Location	chr1:209741188-209741189
allele	A/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	FOS	chr1:209741117-209741525	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:209741060-209741510	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr1:209741061-209741386	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr1:209740665-209741751	SK-N-SH	brain:	n/a	n/a
5	SIN3AK20	chr1:209741002-209741511	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr1:209740787-209741727	SK-N-SH	brain:	n/a	n/a
7	USF1	chr1:209740877-209741424	SK-N-SH	brain:	n/a	n/a
8	USF2	chr1:209741061-209741221	Hela-S3	cervix:	n/a	chr1:209741083-209741094
9	MAX	chr1:209740830-209741698	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr1:209740807-209741804	SK-N-SH	brain:	n/a	n/a
11	TAF1	chr1:209740962-209741352	SK-N-SH	brain:	n/a	n/a
12	YY1	chr1:209740959-209741468	SK-N-SH	brain:	n/a	n/a
13	JUND	chr1:209740869-209741740	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr1:209740814-209741712	SK-N-SH	brain:	n/a	n/a
15	USF1	chr1:209740850-209741322	SK-N-SH_RA	brain:	n/a	n/a
16	TEAD4	chr1:209740949-209741751	SK-N-SH	brain:	n/a	n/a
17	STAT3	chr1:209741128-209741529	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA3	chr1:209740820-209741720	SK-N-SH	brain:	n/a	n/a
19	TCF12	chr1:209740784-209741721	SK-N-SH	brain:	n/a	n/a
20	REST	chr1:209741019-209741277	SK-N-SH	brain:	n/a	n/a
21	TEAD4	chr1:209740977-209741513	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr1:209740773-209741721	SK-N-SH	brain:	n/a	n/a
23	EP300	chr1:209740842-209741727	SK-N-SH	brain:	n/a	n/a
24	JUND	chr1:209740906-209741667	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr1:209740858-209741853	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:209740978-209741416	SK-N-SH	brain:	n/a	n/a
27	FOS	chr1:209741097-209741518	MCF10A-Er-Src	breast:	n/a	n/a
28	MAX	chr1:209740943-209741508	SK-N-SH	brain:	n/a	n/a
29	FOS	chr1:209741087-209741525	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr1:209741115-209741499	MCF10A-Er-Src	breast:	n/a	n/a
31	TEAD4	chr1:209740986-209741412	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr1:209740965-209741601	SK-N-SH_RA	brain:	n/a	n/a
33	POLR2A	chr1:209740885-209741573	SK-N-SH	brain:	n/a	n/a
34	EP300	chr1:209740957-209741631	SK-N-SH_RA	brain:	n/a	n/a
35	USF1	chr1:209740825-209741268	SK-N-SH_RA	brain:	n/a	n/a
36	TEAD4	chr1:209740876-209741712	SK-N-SH	brain:	n/a	n/a
37	FOSL2	chr1:209740909-209741662	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000224260	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10489338	0.83[ASN][1000 genomes]
rs11119309	0.83[ASN][1000 genomes]
rs12084657	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014744	0.85[EUR][1000 genomes]
rs17014768	0.91[EUR][1000 genomes]
rs17014769	0.91[EUR][1000 genomes]
rs17014799	0.83[ASN][1000 genomes]
rs17014808	0.83[ASN][1000 genomes]
rs17014810	0.88[EUR][1000 genomes]
rs17014820	0.88[EUR][1000 genomes]
rs17014822	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17014823	0.88[EUR][1000 genomes]
rs17014830	0.87[EUR][1000 genomes]
rs17014836	0.86[EUR][1000 genomes]
rs17388107	0.90[EUR][1000 genomes]
rs2067744	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55688212	0.86[EUR][1000 genomes]
rs55709381	0.88[EUR][1000 genomes]
rs55967608	0.88[EUR][1000 genomes]
rs56025154	0.86[EUR][1000 genomes]
rs56165413	0.87[EUR][1000 genomes]
rs58987909	0.89[EUR][1000 genomes]
rs60686175	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61819949	0.88[EUR][1000 genomes]
rs61822168	0.89[EUR][1000 genomes]
rs61822169	0.90[EUR][1000 genomes]
rs61822171	0.88[EUR][1000 genomes]
rs61822172	0.88[EUR][1000 genomes]
rs6540543	0.89[EUR][1000 genomes]
rs6669549	0.89[EUR][1000 genomes]
rs6698127	0.88[EUR][1000 genomes]
rs742253	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7512091	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516885	0.86[EUR][1000 genomes]
rs7536585	0.91[EUR][1000 genomes]
rs9430000	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209738200-209742000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209738400-209742000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:209738400-209743000	Weak transcription	Fetal Kidney	kidney
4	chr1:209739000-209741800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:209739200-209741600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:209739600-209741600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:209739600-209743000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:209739800-209743000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:209740200-209741800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:209740400-209741200	Enhancers	NH-A	brain
11	chr1:209740600-209741200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:209740600-209741200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:209740600-209741400	Flanking Active TSS	NHEK	skin
14	chr1:209740600-209741600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:209740600-209741600	Enhancers	HSMM	muscle
16	chr1:209740600-209741600	Enhancers	HSMMtube	muscle
17	chr1:209740600-209742000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:209740800-209741200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:209740800-209741200	Enhancers	Osteobl	bone
20	chr1:209741000-209741200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:209741000-209741200	Enhancers	Esophagus	oesophagus
22	chr1:209741000-209742400	Enhancers	HMEC	breast

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