Variant report

Variant	rs11746675
Chromosome Location	chr5:178413947-178413948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2067011	0.94[ASW][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.86[AFR][1000 genomes]
rs2256966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2645339	0.94[ASW][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs762724	0.81[CHB][hapmap]
rs762725	0.94[ASW][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1017941	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv537974	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv600490	chr5:178405251-178430375	Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv527183	chr5:178409285-178415937	ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv516324	chr5:178410538-178415937	ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv883221	chr5:178410538-178454118	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11746675	MGAT1	cis	cerebellum	SCAN
rs11746675	MXD3	cis	cerebellum	SCAN
rs11746675	ZNF879	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
2	chr5:178401000-178414600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr5:178402000-178414400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr5:178405400-178418200	ZNF genes & repeats	Brain Germinal Matrix	brain
5	chr5:178410000-178414600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:178413000-178417400	ZNF genes & repeats	Fetal Stomach	stomach
7	chr5:178413200-178417200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr5:178413800-178414400	ZNF genes & repeats	Brain Anterior Caudate	brain

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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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