Variant report

Variant	rs3864269
Chromosome Location	chr5:106936965-106936966
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	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: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10045552	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10061771	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10479400	0.91[ASN][1000 genomes]
rs10479401	0.91[ASN][1000 genomes]
rs12153493	1.00[JPT][hapmap]
rs12654557	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656108	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12719573	0.91[ASN][1000 genomes]
rs1990993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005103	1.00[CHB][hapmap]
rs2406374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34052514	0.83[ASN][1000 genomes]
rs34273069	0.91[ASN][1000 genomes]
rs34644687	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34950197	0.91[ASN][1000 genomes]
rs3844311	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4145099	0.84[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4957704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs597083	0.90[GIH][hapmap]
rs62355632	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355633	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641406	0.87[CHD][hapmap]
rs6888055	0.87[CHD][hapmap]
rs6894162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs872240	1.00[CHB][hapmap];1.00[CHD][hapmap]

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:30 , 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	chr5:106929200-106937800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:106929200-106937800	Weak transcription	Fetal Brain Female	brain
6	chr5:106929400-106937800	Weak transcription	Fetal Brain Male	brain
7	chr5:106929400-106945400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:106930600-106939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:106930600-106939800	Weak transcription	Left Ventricle	heart
10	chr5:106930600-106944200	Weak transcription	Esophagus	oesophagus
11	chr5:106930800-106940000	Weak transcription	HMEC	breast
12	chr5:106930800-106940400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:106930800-106940600	Weak transcription	HSMM	muscle
14	chr5:106933400-106952600	Weak transcription	Aorta	Aorta
15	chr5:106933600-106940600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:106934400-106941000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:106935000-106941400	Weak transcription	HUVEC	blood vessel
18	chr5:106935600-106940600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:106935800-106937200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:106935800-106942600	Enhancers	Fetal Heart	heart
21	chr5:106935800-106942800	Weak transcription	Fetal Kidney	kidney
22	chr5:106936000-106937800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:106936000-106941400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:106936200-106938000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:106936200-106938200	Weak transcription	GM12878-XiMat	blood
26	chr5:106936200-106939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:106936200-106941400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:106936600-106937000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:106936600-106937200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:106936800-106939600	Enhancers	A549	lung

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