Variant report

Variant	rs103840
Chromosome Location	chr5:106914733-106914734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106914216..106916170-chr5:106926052..106928145,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12514540	0.96[ASN][1000 genomes]
rs12656108	0.81[ASN][1000 genomes]
rs12656960	0.96[ASN][1000 genomes]
rs2005103	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4145099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs591470	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs607976	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs641406	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6596741	0.96[ASN][1000 genomes]
rs6596742	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs685820	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6879546	0.98[ASN][1000 genomes]
rs6888055	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7734574	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs7737882	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs872240	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]
rs9328010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686509	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs975690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106899400-106915600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:106908200-106916600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:106908800-106917000	Weak transcription	HSMM	muscle
4	chr5:106908800-106917600	Enhancers	A549	lung
5	chr5:106909000-106917000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:106911000-106914800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:106911400-106915200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:106911400-106915600	Enhancers	Fetal Lung	lung
9	chr5:106911800-106914800	Enhancers	NHEK	skin
10	chr5:106911800-106915000	Enhancers	Adipose Nuclei	Adipose
11	chr5:106912200-106916600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:106912200-106917600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:106913400-106915000	Enhancers	GM12878-XiMat	blood
14	chr5:106913400-106916800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:106913600-106914800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:106913600-106916800	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:106913600-106917000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:106913600-106917200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:106913600-106928800	Weak transcription	Right Ventricle	heart
20	chr5:106913800-106915000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:106913800-106915000	Enhancers	NHDF-Ad	bronchial
22	chr5:106913800-106916600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:106913800-106916800	Weak transcription	Fetal Stomach	stomach
24	chr5:106913800-106917000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:106913800-106924000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:106914000-106916600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:106914000-106916800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:106914000-106916800	Weak transcription	Fetal Heart	heart
29	chr5:106914000-106917000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:106914000-106917200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:106914000-106924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:106914200-106914800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:106914200-106917000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:106914200-106924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:106914400-106914800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:106914400-106915600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:106914400-106916400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:106914600-106914800	Enhancers	Left Ventricle	heart
39	chr5:106914600-106915400	Enhancers	Fetal Kidney	kidney
40	chr5:106914600-106916400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:106914600-106916600	Weak transcription	HMEC	breast
42	chr5:106914600-106916600	Weak transcription	Osteobl	bone
43	chr5:106914600-106919200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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