Variant report

Variant	rs1040939
Chromosome Location	chr6:44513341-44513342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1322651	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1475146	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141996	1.00[ASN][1000 genomes]
rs4437456	1.00[ASW][hapmap];0.81[GIH][hapmap]
rs4532440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914011	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9472297	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5283	chr6:44505982-44517131	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv3499026	chr6:44510424-44516522	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv3499029	chr6:44510824-44516422	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv3499031	chr6:44511098-44516312	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv3472517	chr6:44511373-44515828	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv3472520	chr6:44511402-44515853	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv3472518	chr6:44511432-44515838	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv3499027	chr6:44511436-44515867	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv3499025	chr6:44511451-44515825	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv3499032	chr6:44511462-44515800	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv3499028	chr6:44511487-44515788	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv3499033	chr6:44511542-44515744	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	esv3472521	chr6:44511546-44515742	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	esv3499034	chr6:44511546-44515742	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	esv14026	chr6:44511814-44515528	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv514358	chr6:44511870-44515110	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	esv2421578	chr6:44513341-44514951	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1040939	DLK2	cis	cerebellum	SCAN
rs1040939	MRPL14	cis	parietal	SCAN
rs1040939	CUL7	cis	parietal	SCAN
rs1040939	TRERF1	cis	cerebellum	SCAN
rs1040939	HSP90AB1	cis	parietal	SCAN
rs1040939	CYP39A1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44511000-44516000	Weak transcription	HSMMtube	muscle
2	chr6:44511000-44516800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:44512800-44513400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:44513000-44513600	Enhancers	H9 Cell Line	embryonic stem cell

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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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