Variant report

Variant	rs6596742
Chromosome Location	chr5:106938267-106938268
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36582196..36585061-chr5:106936352..106938833,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260025	Chromatin interaction
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs103840	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs12514540	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12656960	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4145099	1.00[CHB][hapmap]
rs607976	0.86[CHB][hapmap]
rs6596741	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879546	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7734574	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7737882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs872240	0.81[CEU][hapmap]
rs9328010	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9686509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs975690	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106926000-106941000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:106928600-106938800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:106929000-106938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:106929400-106945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:106930600-106939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:106930600-106939800	Weak transcription	Left Ventricle	heart
7	chr5:106930600-106944200	Weak transcription	Esophagus	oesophagus
8	chr5:106930800-106940000	Weak transcription	HMEC	breast
9	chr5:106930800-106940400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:106930800-106940600	Weak transcription	HSMM	muscle
11	chr5:106933400-106952600	Weak transcription	Aorta	Aorta
12	chr5:106933600-106940600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:106934400-106941000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:106935000-106941400	Weak transcription	HUVEC	blood vessel
15	chr5:106935600-106940600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:106935800-106942600	Enhancers	Fetal Heart	heart
17	chr5:106935800-106942800	Weak transcription	Fetal Kidney	kidney
18	chr5:106936000-106941400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:106936200-106939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:106936200-106941400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:106936800-106939600	Enhancers	A549	lung
22	chr5:106937000-106938800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:106937200-106940400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:106937200-106942800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:106937800-106939800	Enhancers	Fetal Brain Female	brain
26	chr5:106937800-106942200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr5:106937800-106942400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:106937800-106944600	Enhancers	Fetal Brain Male	brain
29	chr5:106938000-106939800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr5:106938200-106938400	Active TSS	Brain Anterior Caudate	brain
31	chr5:106938200-106938600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:106938200-106938600	Active TSS	Hela-S3	cervix
33	chr5:106938200-106938800	Enhancers	GM12878-XiMat	blood
34	chr5:106938200-106938800	Active TSS	NHDF-Ad	bronchial
35	chr5:106938200-106939200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:106938200-106941000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:106938200-106942600	Enhancers	HUES48 Cell Line	embryonic stem cell

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