Variant report

Variant	rs9543929
Chromosome Location	chr13:76021251-76021252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs4331237	0.83[ASN][1000 genomes]
rs4331238	0.91[ASN][1000 genomes]
rs4369537	0.94[ASN][1000 genomes]
rs4530003	0.92[ASN][1000 genomes]
rs4597197	0.92[ASN][1000 genomes]
rs718147	0.92[ASN][1000 genomes]
rs7334537	0.92[ASN][1000 genomes]
rs7983963	0.88[ASN][1000 genomes]
rs7985929	0.88[ASN][1000 genomes]
rs7995759	0.91[ASN][1000 genomes]
rs9318345	0.89[ASN][1000 genomes]
rs9530437	0.82[ASN][1000 genomes]
rs9530438	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9543927	0.82[ASN][1000 genomes]
rs9543928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9565163	0.88[AMR][1000 genomes]
rs9573541	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9573572	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv455987	chr13:75972846-76090084	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv562346	chr13:75972846-76090084	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9543929	BTF3L1	cis	parietal	SCAN
rs9543929	UCHL3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76007400-76032000	Weak transcription	Gastric	stomach
2	chr13:76012000-76033000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:76012800-76036000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:76014800-76021800	Enhancers	HepG2	liver
5	chr13:76017800-76033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:76017800-76039400	Weak transcription	Fetal Stomach	stomach
7	chr13:76018200-76022200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr13:76020400-76021400	Enhancers	Adipose Nuclei	Adipose
9	chr13:76020400-76021400	Enhancers	Liver	Liver
10	chr13:76020400-76021400	Enhancers	Hela-S3	cervix
11	chr13:76020400-76021800	Enhancers	Fetal Heart	heart
12	chr13:76020400-76030200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr13:76020400-76054400	Weak transcription	A549	lung
14	chr13:76020800-76021600	Weak transcription	Osteobl	bone
15	chr13:76020800-76022000	Enhancers	Psoas Muscle	Psoas
16	chr13:76020800-76022000	Enhancers	Right Ventricle	heart
17	chr13:76021000-76021600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:76021000-76021800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr13:76021000-76022000	Enhancers	Left Ventricle	heart
20	chr13:76021000-76026200	Weak transcription	NHEK	skin
21	chr13:76021200-76021400	Enhancers	Ovary	ovary
22	chr13:76021200-76021600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr13:76021200-76022000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr13:76021200-76026200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:76021200-76026400	Weak transcription	HSMM	muscle
26	chr13:76021200-76026400	Weak transcription	HSMMtube	muscle
27	chr13:76021200-76026800	Weak transcription	Right Atrium	heart

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