Variant report

Variant	rs10507838
Chromosome Location	chr13:76462058-76462059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10507836	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10507837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12869260	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1318553	0.91[EUR][1000 genomes]
rs17065177	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17657837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17713028	0.84[EUR][1000 genomes]
rs17714871	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34440314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34674775	0.91[EUR][1000 genomes]
rs34832254	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34897927	0.98[EUR][1000 genomes]
rs34902046	0.91[EUR][1000 genomes]
rs34959967	0.91[EUR][1000 genomes]
rs34973043	0.91[EUR][1000 genomes]
rs35254061	0.88[EUR][1000 genomes]
rs617686	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs625033	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs71434812	0.91[EUR][1000 genomes]
rs71434813	0.93[EUR][1000 genomes]
rs71434814	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71434815	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs727020	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7988661	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7988841	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7991366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7993408	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7997504	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7997894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9600584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9600585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9600586	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1054431	chr13:76460431-76885094	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv541837	chr13:76460431-76885094	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10507838	TBC1D4	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76440000-76469200	Weak transcription	HSMM	muscle
2	chr13:76451800-76463600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:76461600-76462600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr13:76461600-76462600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr13:76461600-76464400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr13:76461600-76466400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:76461800-76462600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr13:76462000-76462200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:76462000-76462400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr13:76462000-76464400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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