Variant report

Variant	rs9429998
Chromosome Location	chr1:209741377-209741378
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	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	MAX	chr1:209740830-209741698	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr1:209740807-209741804	SK-N-SH	brain:	n/a	n/a
10	FOS	chr1:209741211-209741459	MCF10A-Er-Src	breast:	n/a	n/a
11	YY1	chr1:209740959-209741468	SK-N-SH	brain:	n/a	n/a
12	JUND	chr1:209740869-209741740	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr1:209740814-209741712	SK-N-SH	brain:	n/a	n/a
14	TEAD4	chr1:209740949-209741751	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr1:209741128-209741529	MCF10A-Er-Src	breast:	n/a	n/a
16	GATA3	chr1:209740820-209741720	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr1:209740784-209741721	SK-N-SH	brain:	n/a	n/a
18	TEAD4	chr1:209740977-209741513	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr1:209740773-209741721	SK-N-SH	brain:	n/a	n/a
20	EP300	chr1:209740842-209741727	SK-N-SH	brain:	n/a	n/a
21	JUND	chr1:209740906-209741667	SK-N-SH	brain:	n/a	n/a
22	PBX3	chr1:209740858-209741853	SK-N-SH	brain:	n/a	n/a
23	STAT3	chr1:209741225-209741428	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:209740978-209741416	SK-N-SH	brain:	n/a	n/a
25	FOS	chr1:209741097-209741518	MCF10A-Er-Src	breast:	n/a	n/a
26	MAX	chr1:209740943-209741508	SK-N-SH	brain:	n/a	n/a
27	FOS	chr1:209741087-209741525	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr1:209741115-209741499	MCF10A-Er-Src	breast:	n/a	n/a
29	TEAD4	chr1:209740986-209741412	ECC-1	luminal epithelium:	n/a	n/a
30	EP300	chr1:209740965-209741601	SK-N-SH_RA	brain:	n/a	n/a
31	POLR2A	chr1:209740885-209741573	SK-N-SH	brain:	n/a	n/a
32	EP300	chr1:209740957-209741631	SK-N-SH_RA	brain:	n/a	n/a
33	TEAD4	chr1:209740876-209741712	SK-N-SH	brain:	n/a	n/a
34	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: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11119312	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576233	0.86[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587591	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589826	0.86[EUR][1000 genomes]
rs12144092	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35913818	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690557	0.83[EUR][1000 genomes]
rs713075	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528698	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532726	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541562	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429816	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9429817	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9429818	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429999	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9429998	RP1-272L16.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:18 , 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	chr1:209740600-209741400	Flanking Active TSS	NHEK	skin
11	chr1:209740600-209741600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:209740600-209741600	Enhancers	HSMM	muscle
13	chr1:209740600-209741600	Enhancers	HSMMtube	muscle
14	chr1:209740600-209742000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:209741000-209742400	Enhancers	HMEC	breast
16	chr1:209741200-209743000	Weak transcription	Osteobl	bone
17	chr1:209741200-209743200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:209741200-209743600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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