Variant report

Variant	rs12236287
Chromosome Location	chr9:93728964-93728965
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	FOS	chr9:93728935-93729245	MCF10A-Er-Src	breast:	n/a	chr9:93729055-93729067
2	FOS	chr9:93728964-93729201	MCF10A-Er-Src	breast:	n/a	chr9:93729055-93729067
3	TCF7L2	chr9:93728803-93729133	MCF-7	breast:	n/a	chr9:93728961-93728975 chr9:93728961-93728975 chr9:93728960-93728976
4	FOS	chr9:93728954-93729244	MCF10A-Er-Src	breast:	n/a	chr9:93729055-93729067
5	E2F4	chr9:93728924-93729299	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr9:93728900-93729242	MCF10A-Er-Src	breast:	n/a	chr9:93729055-93729067
7	MYC	chr9:93728957-93729210	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93728320..93731079-chr9:93741313..93742989,2	MCF-7	breast:
2	chr9:93727940..93730376-chr9:93733841..93735595,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228216	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10115615	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10121625	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10465159	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10820823	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10820824	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10991703	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10991704	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10991705	0.82[EUR][1000 genomes]
rs10991729	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10991734	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12352804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13294492	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2184540	1.00[YRI][hapmap]
rs28425571	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36034099	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4452924	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7030712	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73653514	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93724200-93736000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:93726200-93730600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr9:93726200-93731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:93726400-93729600	Enhancers	NHDF-Ad	bronchial
5	chr9:93726400-93730200	Enhancers	NH-A	brain
6	chr9:93726400-93730400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:93726600-93729600	Enhancers	Esophagus	oesophagus
8	chr9:93726800-93730800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:93727000-93729200	Weak transcription	GM12878-XiMat	blood
10	chr9:93727200-93729200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:93727200-93735800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:93727400-93729000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:93727400-93729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:93727600-93729200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:93727600-93729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:93727600-93729200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:93727600-93729600	Enhancers	NHEK	skin
18	chr9:93727600-93729800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:93727800-93730400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:93728000-93729000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:93728000-93729400	Enhancers	Osteobl	bone
22	chr9:93728000-93729800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:93728200-93729200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:93728200-93729600	Enhancers	HMEC	breast
25	chr9:93728200-93730600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:93728200-93733400	Weak transcription	Aorta	Aorta
27	chr9:93728400-93729400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:93728600-93729600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:93728600-93729600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:93728600-93729600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:93728600-93730200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr9:93728600-93732800	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:93728600-93732800	Weak transcription	Fetal Stomach	stomach
34	chr9:93728800-93729000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:93728800-93729600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:93728800-93729600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:93728800-93729800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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