Variant report

Variant	rs9686509
Chromosome Location	chr5:106935029-106935030
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106921384..106923070-chr5:106934624..106936760,2	K562	blood:
2	chr5:106923687..106925505-chr5:106932588..106935068,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs103840	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]
rs12514540	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656108	0.85[ASN][1000 genomes]
rs12656960	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MKK][hapmap];0.83[ASN][1000 genomes]
rs591470	0.86[CHB][hapmap]
rs607976	0.86[CHB][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap]
rs641406	0.89[GIH][hapmap];0.86[MEX][hapmap]
rs6596741	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596742	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]
rs6879546	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6888055	0.85[GIH][hapmap];0.90[MEX][hapmap]
rs7734574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872240	0.85[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs9328010	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs975690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9686509	RPL13AP6	trans	parietal	SCAN

Chromatin state (count:28 , 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	chr5:106930600-106935400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:106930600-106935400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:106930600-106936600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:106930600-106939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:106930600-106939800	Weak transcription	Left Ventricle	heart
13	chr5:106930600-106944200	Weak transcription	Esophagus	oesophagus
14	chr5:106930800-106935800	Weak transcription	Fetal Heart	heart
15	chr5:106930800-106940000	Weak transcription	HMEC	breast
16	chr5:106930800-106940400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:106930800-106940600	Weak transcription	HSMM	muscle
18	chr5:106931400-106935400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:106933200-106935800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:106933400-106952600	Weak transcription	Aorta	Aorta
21	chr5:106933600-106940600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:106934200-106935200	Enhancers	HepG2	liver
23	chr5:106934400-106935200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr5:106934400-106935400	Flanking Active TSS	A549	lung
25	chr5:106934400-106941000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:106934800-106935200	Enhancers	Stomach Mucosa	stomach
27	chr5:106934800-106935400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:106935000-106941400	Weak transcription	HUVEC	blood vessel

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