Variant report

Variant	rs6889555
Chromosome Location	chr5:167677870-167677871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10447194	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10447203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11134498	0.96[ASN][1000 genomes]
rs11740056	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11740804	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11743769	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11743857	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11743859	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11747056	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12189266	0.97[ASN][1000 genomes]
rs13164502	0.97[ASN][1000 genomes]
rs2112553	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112554	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2173017	0.97[ASN][1000 genomes]
rs2337158	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35200122	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35960642	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976587	0.96[ASN][1000 genomes]
rs62385563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385591	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6868169	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6876164	0.81[AMR][1000 genomes]
rs6876197	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6888941	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6895245	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72835080	0.98[ASN][1000 genomes]

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	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv5117	chr5:167666701-167711857	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv462512	chr5:167672105-167702041	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv600257	chr5:167672105-167702041	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 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	chr5:167646800-167695800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:167661600-167688200	Weak transcription	HMEC	breast
3	chr5:167666400-167682600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:167667200-167679200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:167668600-167679600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:167672200-167695800	Weak transcription	Fetal Heart	heart
7	chr5:167673000-167678000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:167673000-167695600	Weak transcription	Brain Anterior Caudate	brain
9	chr5:167673400-167679200	Strong transcription	NHEK	skin
10	chr5:167674400-167695800	Weak transcription	Fetal Lung	lung
11	chr5:167674600-167694400	Weak transcription	Fetal Brain Male	brain
12	chr5:167674800-167678400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:167674800-167696000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:167675000-167686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:167675000-167695800	Weak transcription	Brain Angular Gyrus	brain
16	chr5:167675400-167681000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:167675400-167696000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:167675400-167696000	Weak transcription	Fetal Brain Female	brain
19	chr5:167675600-167678000	Weak transcription	Brain Germinal Matrix	brain
20	chr5:167675600-167678200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:167675600-167687200	Weak transcription	Right Ventricle	heart
22	chr5:167675600-167687400	Weak transcription	Left Ventricle	heart
23	chr5:167675800-167696000	Weak transcription	HSMM	muscle
24	chr5:167676600-167687200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:167676800-167678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:167677600-167678800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:167677600-167679000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:167677800-167678400	Enhancers	NH-A	brain
29	chr5:167677800-167679000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:167677800-167679200	Enhancers	Cortex derived primary cultured neurospheres	brain

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