Variant report

Variant	rs872240
Chromosome Location	chr5:106918212-106918213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106911881..106914239-chr5:106916867..106919606,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10045552	1.00[CHB][hapmap]
rs10061771	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs103840	0.82[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1990993	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2005103	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844311	1.00[CHB][hapmap]
rs3864269	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4957704	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs591470	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs607976	0.82[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs641406	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6596742	0.81[CEU][hapmap]
rs685820	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6888055	0.88[ASW][hapmap];0.82[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6894162	1.00[CHB][hapmap]
rs7734574	0.85[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap]
rs7737882	0.85[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs9328010	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9686509	0.85[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs975690	0.85[CEU][hapmap]

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	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2633190	chr5:106917311-106918910	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106913600-106928800	Weak transcription	Right Ventricle	heart
2	chr5:106913800-106924000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:106914000-106924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:106914200-106924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:106914600-106919200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:106914800-106928200	Weak transcription	Left Ventricle	heart
7	chr5:106915200-106929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:106915600-106928200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:106916800-106918400	Enhancers	Fetal Heart	heart
10	chr5:106917000-106921400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:106917000-106929200	Weak transcription	HMEC	breast
12	chr5:106917400-106918400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:106917400-106924200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:106917400-106928000	Weak transcription	HSMMtube	muscle
15	chr5:106917600-106918400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:106917600-106919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:106917600-106923600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:106917600-106928200	Weak transcription	A549	lung
19	chr5:106917800-106928600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:106918200-106919200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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