Variant report

Variant	rs10982544
Chromosome Location	chr9:117877063-117877064
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	FOS	chr9:117876909-117877337	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:117858058-117881674	U87	brain:	n/a	n/a
3	TCF12	chr9:117876500-117877283	ECC-1	luminal epithelium:	n/a	chr9:117876898-117876905
4	EP300	chr9:117876787-117877270	SK-N-SH_RA	brain:	n/a	n/a
5	ESR1	chr9:117876594-117877158	ECC-1	luminal epithelium:	n/a	n/a
6	STAT3	chr9:117876331-117877270	MCF10A-Er-Src	breast:	n/a	n/a
7	GATA3	chr9:117876789-117879555	SK-N-SH	brain:	n/a	chr9:117878767-117878775
8	FOS	chr9:117876905-117878643	MCF10A-Er-Src	breast:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
9	EP300	chr9:117876332-117877920	ECC-1	luminal epithelium:	n/a	n/a
10	PBX3	chr9:117876922-117877671	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr9:117876852-117879384	SK-N-SH	brain:	n/a	chr9:117876898-117876905
12	NFIC	chr9:117876738-117877288	ECC-1	luminal epithelium:	n/a	n/a
13	FOSL2	chr9:117876760-117877845	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr9:117876380-117877345	MCF10A-Er-Src	breast:	n/a	n/a
15	FOXM1	chr9:117876452-117877837	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr9:117876849-117877141	SK-N-SH	brain:	n/a	n/a
17	FOS	chr9:117877027-117877227	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr9:117876991-117877249	MCF10A-Er-Src	breast:	n/a	n/a
19	JUND	chr9:117876669-117878747	SK-N-SH	brain:	n/a	chr9:117877962-117877973 chr9:117877960-117877970 chr9:117877960-117877970 chr9:117877961-117877969 chr9:117877960-117877970 chr9:117877960-117877970
20	PBX3	chr9:117876809-117878207	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr9:117876174-117879494	SK-N-SH	brain:	n/a	chr9:117876898-117876905
22	EP300	chr9:117876905-117877222	SK-N-SH_RA	brain:	n/a	n/a
23	EP300	chr9:117876734-117877832	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr9:117876849-117879682	SK-N-SH	brain:	n/a	n/a
25	NFIC	chr9:117876547-117877700	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr9:117863693-117881740	U87	brain:	n/a	n/a
27	NFIC	chr9:117876700-117879564	SK-N-SH	brain:	n/a	n/a
28	STAT3	chr9:117876649-117877339	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10982514	1.00[CEU][hapmap]
rs10982515	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982537	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10982542	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10982543	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12380780	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1250028	1.00[CEU][hapmap]
rs1757095	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7853005	0.82[AMR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:117862600-117877200	Weak transcription	Fetal Kidney	kidney
3	chr9:117862600-117877200	Weak transcription	Fetal Stomach	stomach
4	chr9:117869200-117878400	Weak transcription	Fetal Lung	lung
5	chr9:117870400-117879000	Weak transcription	Esophagus	oesophagus
6	chr9:117874600-117877600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:117875400-117879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:117875800-117877200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:117876000-117877800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:117876000-117878200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:117876000-117878200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
12	chr9:117876000-117879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:117876200-117878200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:117876400-117877600	Genic enhancers	NHEK	skin
15	chr9:117876400-117877800	Enhancers	HMEC	breast
16	chr9:117876400-117878200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:117876400-117880200	Enhancers	Hela-S3	cervix
18	chr9:117876600-117877200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:117876600-117877400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:117876600-117877600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr9:117876600-117877600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:117876600-117878600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:117876600-117879000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
24	chr9:117876800-117877200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
25	chr9:117876800-117877400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:117876800-117877400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:117876800-117877400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:117876800-117877400	Enhancers	Rectal Smooth Muscle	rectum
29	chr9:117876800-117877400	Genic enhancers	NHDF-Ad	bronchial
30	chr9:117876800-117877400	Genic enhancers	NHLF	lung
31	chr9:117876800-117877600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr9:117876800-117877600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:117876800-117877600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:117876800-117877800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr9:117876800-117879000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr9:117876800-117879200	Enhancers	HSMM	muscle
37	chr9:117877000-117877200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:117877000-117877400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:117877000-117877400	Enhancers	Colon Smooth Muscle	Colon
40	chr9:117877000-117877400	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr9:117877000-117877600	Weak transcription	Aorta	Aorta
42	chr9:117877000-117878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:117877000-117879400	Flanking Active TSS	NH-A	brain

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