Variant report

Variant	rs13407457
Chromosome Location	chr2:11655487-11655488
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	ESR1	chr2:11655465-11655983	ECC-1	luminal epithelium:	n/a	chr2:11655832-11655847
2	ESR1	chr2:11655477-11655903	ECC-1	luminal epithelium:	n/a	chr2:11655832-11655847

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11634128..11636998-chr2:11655433..11657027,2	K562	blood:
2	chr2:11638401..11639245-chr2:11655378..11656188,4	MCF-7	breast:

Variant related genes	Relation type
RNA5SP84	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10169987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10174895	0.86[ASN][1000 genomes]
rs10192123	0.86[ASN][1000 genomes]
rs10201673	0.86[ASN][1000 genomes]
rs10205078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10929750	0.86[ASN][1000 genomes]
rs11897533	0.86[ASN][1000 genomes]
rs12165170	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13383410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13395155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407702	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13418262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424905	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432124	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13432756	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1595018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16857565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002730	0.86[ASN][1000 genomes]
rs2043542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2082829	0.86[ASN][1000 genomes]
rs2082830	0.86[ASN][1000 genomes]
rs4668729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4669737	0.86[ASN][1000 genomes]
rs4669739	0.86[ASN][1000 genomes]
rs4669740	0.86[ASN][1000 genomes]
rs61362255	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432202	1.00[CHB][hapmap]
rs6432209	0.86[ASN][1000 genomes]
rs6719003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6719009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6739168	0.86[ASN][1000 genomes]
rs6741736	0.86[ASN][1000 genomes]
rs6756327	0.86[ASN][1000 genomes]
rs73187472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580473	0.99[EUR][1000 genomes]
rs7597108	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875231	0.86[ASN][1000 genomes]
rs877164	0.86[ASN][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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11647000-11664400	Weak transcription	Right Ventricle	heart
2	chr2:11647000-11665800	Weak transcription	Right Atrium	heart
3	chr2:11648800-11655600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:11648800-11655600	Weak transcription	Fetal Stomach	stomach
5	chr2:11651000-11655800	Enhancers	HepG2	liver
6	chr2:11651200-11658200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:11651400-11657000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:11652600-11656200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:11652600-11656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:11653200-11656200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:11653200-11656600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:11653400-11657400	Enhancers	Ovary	ovary
13	chr2:11653600-11656000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:11653600-11656000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:11654000-11656600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:11654000-11664000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:11654400-11656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:11654600-11655600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:11654800-11664400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:11655000-11657000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:11655000-11657600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:11655200-11656200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:11655400-11655600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:11655400-11656200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:11655400-11656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:11655400-11656600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:11655400-11657600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:11655400-11664000	Weak transcription	H9 Cell Line	embryonic stem cell

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