Variant report

Variant	rs6562924
Chromosome Location	chr13:76452473-76452474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11149001	0.88[AMR][1000 genomes]
rs1359113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120062	0.88[AMR][1000 genomes]
rs2120063	0.88[AMR][1000 genomes]
rs4885354	0.82[EUR][1000 genomes]
rs4885364	0.88[AMR][1000 genomes]
rs6562925	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7986131	0.84[EUR][1000 genomes]
rs7986288	0.91[CEU][hapmap]
rs7992520	0.88[AMR][1000 genomes]
rs7995442	0.82[EUR][1000 genomes]
rs7996791	0.81[CEU][hapmap]
rs9530485	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9544057	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6562924	TBC1D4	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76440000-76469200	Weak transcription	HSMM	muscle
2	chr13:76445400-76454400	Weak transcription	Osteobl	bone
3	chr13:76445600-76453400	Weak transcription	Adipose Nuclei	Adipose
4	chr13:76445600-76453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:76451000-76452600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:76451200-76452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:76451200-76453800	Weak transcription	Colon Smooth Muscle	Colon
8	chr13:76451200-76454000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:76451200-76454800	Weak transcription	Fetal Stomach	stomach
10	chr13:76451400-76454800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:76451400-76455000	Weak transcription	Fetal Kidney	kidney
12	chr13:76451400-76455000	Weak transcription	Fetal Lung	lung
13	chr13:76451600-76454800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr13:76451600-76455400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr13:76451800-76463600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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