Variant report

Variant	rs2023879
Chromosome Location	chr7:51038202-51038203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1018941	0.82[AMR][1000 genomes]
rs1018942	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1018979	0.82[AMR][1000 genomes]
rs1018980	0.82[AMR][1000 genomes]
rs1024472	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10262964	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11765215	0.82[AMR][1000 genomes]
rs12534954	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13310888	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1859264	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1859265	0.82[AMR][1000 genomes]
rs1859477	0.82[AMR][1000 genomes]
rs1989265	0.82[AMR][1000 genomes]
rs2189428	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2189429	0.82[AMR][1000 genomes]
rs2214494	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2214495	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2214497	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329569	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4947530	0.82[AMR][1000 genomes]
rs4948086	0.82[AMR][1000 genomes]
rs4948088	0.82[AMR][1000 genomes]
rs4948146	0.82[AMR][1000 genomes]
rs6943902	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6961183	1.00[CEU][hapmap]
rs6971609	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979183	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs720068	0.82[AMR][1000 genomes]
rs7803628	0.82[AMR][1000 genomes]
rs886437	0.82[AMR][1000 genomes]
rs917073	0.82[AMR][1000 genomes]
rs976088	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv606907	chr7:50899168-51195380	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv888022	chr7:50933678-51046674	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2761146	chr7:50975457-51957019	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1027122	chr7:50984824-51376078	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv538836	chr7:50984824-51376078	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv830999	chr7:51020735-51164809	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2023879	BCAR3	trans	brain	seeQTL
rs2023879	FBXO30	trans	brain	seeQTL
rs2023879	PASK	trans	brain	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:51035400-51041600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:51037400-51041000	Enhancers	Pancreas	Pancrea
3	chr7:51038000-51049600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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