Variant report

Variant	rs6888941
Chromosome Location	chr5:167686657-167686658
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10447194	0.97[ASN][1000 genomes]
rs10447203	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11134498	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740056	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740804	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743857	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743859	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11959012	0.89[CEU][hapmap]
rs12189266	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13164502	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17632540	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs2112553	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2112554	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2173017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2337158	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35200122	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35960642	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4976587	0.99[ASN][1000 genomes]
rs62385563	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62385591	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868169	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6889555	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72835080	0.96[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:29 , 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	chr5:167672200-167695800	Weak transcription	Fetal Heart	heart
4	chr5:167673000-167695600	Weak transcription	Brain Anterior Caudate	brain
5	chr5:167674400-167695800	Weak transcription	Fetal Lung	lung
6	chr5:167674600-167694400	Weak transcription	Fetal Brain Male	brain
7	chr5:167674800-167696000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:167675000-167695800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:167675400-167696000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:167675400-167696000	Weak transcription	Fetal Brain Female	brain
11	chr5:167675600-167687200	Weak transcription	Right Ventricle	heart
12	chr5:167675600-167687400	Weak transcription	Left Ventricle	heart
13	chr5:167675800-167696000	Weak transcription	HSMM	muscle
14	chr5:167676600-167687200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:167678600-167687200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:167678800-167696000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:167678800-167696000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:167679000-167696000	Weak transcription	Brain Germinal Matrix	brain
19	chr5:167679200-167695600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:167679600-167694800	Weak transcription	HSMMtube	muscle
21	chr5:167680800-167692000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:167681200-167687200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:167682600-167686800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:167684000-167690400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:167685800-167687000	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:167686400-167689000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:167686400-167689200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:167686600-167689200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:167686600-167690800	Strong transcription	NHEK	skin

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