Variant report

Variant	rs16878193
Chromosome Location	chr5:59806470-59806471
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10036678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10044835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10045093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074908	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10939850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509215	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857232	0.91[ASN][1000 genomes]
rs7723306	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7729652	0.90[ASN][1000 genomes]
rs7729781	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59801400-59813800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:59801800-59813000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:59802000-59806800	Enhancers	GM12878-XiMat	blood
4	chr5:59802400-59812400	Weak transcription	Primary B cells from cord blood	blood
5	chr5:59803600-59807200	Enhancers	Rectal Smooth Muscle	rectum
6	chr5:59804200-59815800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:59805200-59806600	Enhancers	Colon Smooth Muscle	Colon
8	chr5:59805200-59807000	Enhancers	Stomach Smooth Muscle	stomach
9	chr5:59805400-59806800	Enhancers	Fetal Muscle Leg	muscle
10	chr5:59805600-59806800	Enhancers	Brain Substantia Nigra	brain
11	chr5:59805800-59806600	Enhancers	Brain Anterior Caudate	brain
12	chr5:59805800-59806800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr5:59805800-59807000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:59805800-59807000	Enhancers	Brain Angular Gyrus	brain
15	chr5:59805800-59807200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:59806000-59806800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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