Variant report

Variant	rs1335332
Chromosome Location	chr9:117884015-117884016
allele	A/C
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	NFIC	chr9:117883098-117884247	ECC-1	luminal epithelium:	n/a	chr9:117883561-117883578
2	TCF12	chr9:117883090-117884104	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr9:117883029-117884239	ECC-1	luminal epithelium:	n/a	n/a
4	GATA3	chr9:117883363-117884067	SK-N-SH	brain:	n/a	chr9:117883662-117883670
5	EP300	chr9:117883012-117884196	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr9:117883195-117884047	SK-N-SH	brain:	n/a	chr9:117883561-117883578
7	FOXM1	chr9:117883133-117884078	ECC-1	luminal epithelium:	n/a	n/a
8	CEBPB	chr9:117883298-117884032	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr9:117883280-117884116	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr9:117883209-117884120	ECC-1	luminal epithelium:	n/a	chr9:117883561-117883578
11	GATA3	chr9:117883246-117884080	SK-N-SH	brain:	n/a	chr9:117883662-117883670
12	TEAD4	chr9:117883113-117884082	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr9:117883228-117884348	ECC-1	luminal epithelium:	n/a	n/a
14	FOXM1	chr9:117883200-117884113	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr9:117883139-117884080	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10125663	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817713	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982553	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414137	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537015	0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1537016	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537720	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4979496	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7853883	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884290	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945256	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs945257	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1335332	COL27A1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117881400-117884400	Enhancers	NH-A	brain
2	chr9:117881400-117886000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr9:117881600-117884200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:117881600-117884200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:117881600-117884400	Enhancers	NHEK	skin
6	chr9:117881800-117884400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:117882000-117888800	Weak transcription	NHLF	lung
8	chr9:117882400-117884400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:117882600-117885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:117882800-117884400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:117883200-117884400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:117883200-117884400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:117883200-117884400	Enhancers	HMEC	breast
14	chr9:117883400-117884400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:117883600-117888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:117883800-117884200	Enhancers	Osteobl	bone
17	chr9:117884000-117884400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:117884000-117887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:117884000-117888800	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:117884000-117892600	Weak transcription	Colon Smooth Muscle	Colon

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