Variant report

Variant	rs13407702
Chromosome Location	chr2:11655684-11655685
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	chr2:11655493-11655918	ECC-1	luminal epithelium:	n/a	chr2:11655832-11655847
2	ESR1	chr2:11655465-11655983	ECC-1	luminal epithelium:	n/a	chr2:11655832-11655847
3	ESR1	chr2:11655477-11655903	ECC-1	luminal epithelium:	n/a	chr2:11655832-11655847
4	ESR1	chr2:11655581-11655875	ECC-1	luminal epithelium:	n/a	chr2:11655832-11655847
5	ESR1	chr2:11655546-11656033	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: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13383410	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13395155	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13407457	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13418262	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13424905	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13430148	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13432124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13432756	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16857565	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61362255	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73187472	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7580473	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7597108	0.88[AMR][1000 genomes];0.99[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:29 , 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	chr2:11651000-11655800	Enhancers	HepG2	liver
4	chr2:11651200-11658200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:11651400-11657000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:11652600-11656200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr2:11652600-11656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:11653200-11656200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr2:11653200-11656600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:11653400-11657400	Enhancers	Ovary	ovary
11	chr2:11653600-11656000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:11653600-11656000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:11654000-11656600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:11654000-11664000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:11654400-11656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:11654800-11664400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:11655000-11657000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:11655000-11657600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11655200-11656200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr2:11655400-11656200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:11655400-11656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:11655400-11656600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:11655400-11657600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:11655400-11664000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:11655600-11656000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:11655600-11656000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:11655600-11656000	Enhancers	Fetal Stomach	stomach
28	chr2:11655600-11656200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:11655600-11656200	Enhancers	Fetal Muscle Leg	muscle

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