Variant report

Variant	rs1537340
Chromosome Location	chr6:12881855-12881856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12526453	1.00[CHD][hapmap]
rs12528956	1.00[CHD][hapmap]
rs12530250	1.00[JPT][hapmap]
rs13201878	0.86[CEU][hapmap];1.00[CHD][hapmap]
rs13208248	0.89[EUR][1000 genomes]
rs13211739	1.00[CHB][hapmap]
rs13219256	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332841	1.00[CHD][hapmap]
rs1332845	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332846	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332847	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327621	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2876300	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944538	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355695	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711863	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4714946	1.00[CHD][hapmap]
rs4714951	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs62389954	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62389955	0.81[EUR][1000 genomes]
rs6458503	1.00[CHD][hapmap]
rs6922782	0.82[CEU][hapmap]
rs71562459	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9296494	1.00[CHD][hapmap]
rs9381500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9472786	1.00[CHD][hapmap]
rs9473086	1.00[CHD][hapmap]

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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription 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	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1537340	NEDD9	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12867400-12887600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:12867600-12886800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:12870400-12885200	Weak transcription	Brain Germinal Matrix	brain
4	chr6:12875400-12885200	Weak transcription	Fetal Brain Female	brain
5	chr6:12880600-12882200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:12880600-12882400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:12881400-12882200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:12881400-12882200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:12881600-12882000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:12881600-12886800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:12881800-12882000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:12881800-12882200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:12881800-12885200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:12881800-12885600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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