Variant report

Variant	rs10982546
Chromosome Location	chr9:117883660-117883661
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	EP300	chr9:117883248-117884014	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr9:117883098-117884247	ECC-1	luminal epithelium:	n/a	chr9:117883561-117883578
3	POLR2A	chr9:117883436-117883852	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr9:117883090-117884104	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr9:117883224-117883871	ECC-1	luminal epithelium:	n/a	n/a
6	PBX3	chr9:117883391-117883964	SK-N-SH	brain:	n/a	n/a
7	NR3C1	chr9:117883362-117883959	ECC-1	luminal epithelium:	n/a	chr9:117883732-117883739
8	TEAD4	chr9:117883302-117883955	SK-N-SH	brain:	n/a	n/a
9	TEAD4	chr9:117883299-117883978	SK-N-SH	brain:	n/a	n/a
10	YY1	chr9:117883193-117883932	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr9:117883029-117884239	ECC-1	luminal epithelium:	n/a	n/a
12	TCF12	chr9:117883335-117883983	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr9:117883247-117883990	ECC-1	luminal epithelium:	n/a	n/a
14	GATA3	chr9:117883363-117884067	SK-N-SH	brain:	n/a	chr9:117883662-117883670
15	FOXA1	chr9:117883369-117883726	ECC-1	luminal epithelium:	n/a	n/a
16	EP300	chr9:117883012-117884196	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr9:117883195-117884047	SK-N-SH	brain:	n/a	chr9:117883561-117883578
18	EP300	chr9:117883490-117883846	SK-N-SH_RA	brain:	n/a	n/a
19	FOXM1	chr9:117883133-117884078	ECC-1	luminal epithelium:	n/a	n/a
20	PBX3	chr9:117883389-117883961	SK-N-SH	brain:	n/a	n/a
21	FOXA1	chr9:117883325-117883795	ECC-1	luminal epithelium:	n/a	n/a
22	CEBPB	chr9:117883298-117884032	ECC-1	luminal epithelium:	n/a	n/a
23	CEBPB	chr9:117883309-117883814	ECC-1	luminal epithelium:	n/a	n/a
24	ESR1	chr9:117883240-117883993	ECC-1	luminal epithelium:	n/a	n/a
25	REST	chr9:117883405-117883792	ECC-1	luminal epithelium:	n/a	n/a
26	TCF12	chr9:117883280-117884116	SK-N-SH	brain:	n/a	n/a
27	NFIC	chr9:117883209-117884120	ECC-1	luminal epithelium:	n/a	chr9:117883561-117883578
28	SRF	chr9:117883235-117883960	ECC-1	luminal epithelium:	n/a	n/a
29	GATA3	chr9:117883246-117884080	SK-N-SH	brain:	n/a	chr9:117883662-117883670
30	EP300	chr9:117883430-117883851	SK-N-SH_RA	brain:	n/a	n/a
31	NR3C1	chr9:117883275-117883919	ECC-1	luminal epithelium:	n/a	chr9:117883732-117883739
32	TEAD4	chr9:117883113-117884082	ECC-1	luminal epithelium:	n/a	n/a
33	TEAD4	chr9:117883228-117884348	ECC-1	luminal epithelium:	n/a	n/a
34	FOXM1	chr9:117883200-117884113	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr9:117883165-117883984	ECC-1	luminal epithelium:	n/a	chr9:117883908-117883917
36	RAD21	chr9:117883473-117883922	SK-N-SH_RA	brain:	n/a	n/a
37	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: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1335330	0.88[CEU][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1335334	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1414138	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1537721	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1537722	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1537727	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1537728	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1591421	0.83[MEX][hapmap]
rs2094941	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2992148	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246907	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4335203	0.87[MEX][hapmap]
rs4978618	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979508	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7030031	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7470092	0.85[ASN][1000 genomes]
rs7847610	0.80[ASN][1000 genomes]
rs884789	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10982546	RGL4	trans	parietal	SCAN
rs10982546	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117881200-117884000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:117881400-117884400	Enhancers	NH-A	brain
3	chr9:117881400-117886000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:117881600-117884200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:117881600-117884200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:117881600-117884400	Enhancers	NHEK	skin
7	chr9:117881800-117883800	Weak transcription	HSMM	muscle
8	chr9:117881800-117884000	Enhancers	Colon Smooth Muscle	Colon
9	chr9:117881800-117884000	Enhancers	Stomach Smooth Muscle	stomach
10	chr9:117881800-117884400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr9:117882000-117888800	Weak transcription	NHLF	lung
12	chr9:117882200-117883800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:117882200-117883800	Weak transcription	Osteobl	bone
14	chr9:117882400-117884400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:117882600-117885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:117882800-117884000	Enhancers	Rectal Smooth Muscle	rectum
17	chr9:117882800-117884400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:117883200-117883800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:117883200-117883800	Enhancers	Brain Germinal Matrix	brain
20	chr9:117883200-117884000	Enhancers	Fetal Muscle Leg	muscle
21	chr9:117883200-117884400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:117883200-117884400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:117883200-117884400	Enhancers	HMEC	breast
24	chr9:117883400-117883800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr9:117883400-117884400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:117883600-117883800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:117883600-117888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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