Variant report

Variant	rs42799
Chromosome Location	chr2:40839928-40839929
allele	G/T
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:11)

rs_ID	r²[population]
rs173804	0.82[EUR][1000 genomes]
rs1861304	0.81[EUR][1000 genomes]
rs1990619	0.81[EUR][1000 genomes]
rs2192812	0.95[YRI][hapmap]
rs42785	0.83[EUR][1000 genomes]
rs42788	0.82[EUR][1000 genomes]
rs42790	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42794	0.83[EUR][1000 genomes]
rs62139541	0.85[ASN][1000 genomes]
rs62139542	0.85[ASN][1000 genomes]
rs6714287	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv456418	chr2:40805427-40848550	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv581505	chr2:40805427-40848550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873918	chr2:40805427-40890416	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv581506	chr2:40809049-40848645	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873919	chr2:40815238-40853317	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv470454	chr2:40815238-40896385	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv456429	chr2:40823026-40896385	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv581507	chr2:40823026-40896385	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv581508	chr2:40833142-40890416	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
14	nsv873920	chr2:40833142-40890416	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
15	nsv581509	chr2:40835285-40857899	Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
16	nsv581510	chr2:40835285-40869165	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
17	nsv873921	chr2:40835285-40869165	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
18	nsv873922	chr2:40835285-40876113	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
19	nsv873923	chr2:40835285-40890416	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
20	nsv873924	chr2:40835285-40926138	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
21	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
22	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv873930	chr2:40837953-40857529	Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
28	nsv581511	chr2:40839418-40863036	Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs42799	FEZ2	cis	cerebellum	SCAN
rs42799	ABCG8	cis	parietal	SCAN
rs42799	TMEM178	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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