Variant report

Variant	rs9287731
Chromosome Location	chr2:11652795-11652796
allele	G/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	FOXM1	chr2:11652614-11653420	MCF-7	breast:	n/a	n/a
2	EP300	chr2:11652601-11653349	MCF-7	breast:	n/a	n/a
3	ESR1	chr2:11652713-11653259	T-47D	breast:	n/a	chr2:11653033-11653050 chr2:11653034-11653051
4	ESR1	chr2:11652779-11653202	ECC-1	luminal epithelium:	n/a	chr2:11653033-11653050 chr2:11653034-11653051
5	EP300	chr2:11652516-11653510	MCF-7	breast:	n/a	n/a
6	POLR2A	chr2:11652622-11653017	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr2:11652501-11653526	MCF-7	breast:	n/a	n/a
8	ESR1	chr2:11652757-11653241	T-47D	breast:	n/a	chr2:11653033-11653050 chr2:11653034-11653051
9	ESR1	chr2:11652784-11653272	T-47D	breast:	n/a	chr2:11653033-11653050 chr2:11653034-11653051
10	ZNF217	chr2:11652780-11653356	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:11652714-11652831	MCF-7	breast:	n/a	n/a
12	FOXM1	chr2:11652634-11653455	MCF-7	breast:	n/a	n/a
13	MAX	chr2:11652617-11653181	MCF-7	breast:	n/a	n/a
14	NR2F2	chr2:11652712-11653400	MCF-7	breast:	n/a	n/a
15	GATA3	chr2:11652681-11653364	MCF-7	breast:	n/a	n/a
16	MYC	chr2:11652773-11652929	MCF-7	breast:	n/a	n/a
17	CEBPB	chr2:11652713-11653328	MCF-7	breast:	n/a	n/a
18	ESR1	chr2:11652763-11653350	ECC-1	luminal epithelium:	n/a	chr2:11653033-11653050 chr2:11653034-11653051
19	ESR1	chr2:11652729-11653200	ECC-1	luminal epithelium:	n/a	chr2:11653033-11653050 chr2:11653034-11653051
20	GATA3	chr2:11652520-11653366	MCF-7	breast:	n/a	n/a
21	MYC	chr2:11652788-11652943	MCF-7	breast:	n/a	n/a
22	TCF12	chr2:11652600-11653636	MCF-7	breast:	n/a	n/a
23	TCF7L2	chr2:11652784-11653185	MCF-7	breast:	n/a	n/a
24	TCF12	chr2:11652595-11653304	MCF-7	breast:	n/a	n/a
25	ESR1	chr2:11652665-11653197	ECC-1	luminal epithelium:	n/a	chr2:11653033-11653050 chr2:11653034-11653051

No.	Distal block	Cell Line	Cell type
1	chr2:11652637..11653514-chr2:11679272..11680297,3	MCF-7	breast:
2	chr2:11638369..11639333-chr2:11652675..11653513,4	MCF-7	breast:
3	chr2:11652487..11653480-chr2:11670844..11671576,4	MCF-7	breast:
4	chr2:11652624..11653481-chr2:11670844..11671697,3	MCF-7	breast:
5	chr2:11652567..11653117-chr2:11672197..11673095,3	MCF-7	breast:
6	chr2:11633169..11635401-chr2:11651358..11653999,2	K562	blood:
7	chr2:11652589..11653514-chr2:11679272..11680302,5	MCF-7	breast:
8	chr2:11638356..11639360-chr2:11652606..11653620,6	MCF-7	breast:
9	chr17:57920653..57922986-chr2:11651115..11653759,2	MCF-7	breast:
10	chr2:11638693..11639199-chr2:11652689..11653318,2	MCF-7	breast:
11	chr2:11652567..11653314-chr2:11672197..11673097,3	MCF-7	breast:
12	chr2:11557290..11560027-chr2:11651365..11653430,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP84	TF binding region
ENSG00000196208	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10191947	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12468776	0.86[EUR][1000 genomes]
rs12477087	0.86[EUR][1000 genomes]
rs13428964	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2043541	0.88[CEU][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs4669742	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6722279	0.86[EUR][1000 genomes]
rs6732810	0.88[EUR][1000 genomes]
rs67894448	0.87[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11639600-11655000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:11641400-11653200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:11641600-11653800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:11646400-11653800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:11647000-11664400	Weak transcription	Right Ventricle	heart
6	chr2:11647000-11665800	Weak transcription	Right Atrium	heart
7	chr2:11648400-11653600	Weak transcription	Brain Germinal Matrix	brain
8	chr2:11648600-11653000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:11648800-11655200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:11648800-11655600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:11648800-11655600	Weak transcription	Fetal Stomach	stomach
12	chr2:11649000-11654000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:11649000-11655400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:11651000-11655800	Enhancers	HepG2	liver
15	chr2:11651200-11658200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:11651400-11655400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr2:11651400-11657000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:11652000-11653800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:11652000-11655000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:11652200-11653200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:11652600-11653000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:11652600-11653400	Flanking Active TSS	Ovary	ovary
23	chr2:11652600-11655400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:11652600-11656200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:11652600-11656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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