Variant report

Variant	rs4758380
Chromosome Location	chr11:6100683-6100684
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11040594	0.81[EUR][1000 genomes]
rs11040648	0.81[EUR][1000 genomes]
rs11040649	0.81[EUR][1000 genomes]
rs11040650	0.81[EUR][1000 genomes]
rs11040652	0.81[EUR][1000 genomes]
rs11040653	0.81[EUR][1000 genomes]
rs11511999	0.80[EUR][1000 genomes]
rs11826453	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1381911	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1599692	1.00[ASN][1000 genomes]
rs1903778	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903779	0.81[ASN][1000 genomes]
rs325634	0.87[ASN][1000 genomes]
rs325639	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.94[ASN][1000 genomes]
rs325640	1.00[JPT][hapmap]
rs325657	0.83[ASN][1000 genomes]
rs325661	0.86[ASN][1000 genomes]
rs325666	0.92[ASN][1000 genomes]
rs325697	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs34220108	0.86[ASN][1000 genomes]
rs3921908	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[ASN][1000 genomes]
rs4362124	0.81[EUR][1000 genomes]
rs4520575	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604856	0.81[EUR][1000 genomes]
rs4758077	0.81[EUR][1000 genomes]
rs4758078	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758079	0.81[EUR][1000 genomes]
rs4758080	0.81[EUR][1000 genomes]
rs4758085	1.00[ASN][1000 genomes]
rs4758086	0.89[ASN][1000 genomes]
rs4758379	0.81[EUR][1000 genomes]
rs4758392	0.94[ASN][1000 genomes]
rs6578740	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6578742	0.83[ASN][1000 genomes]
rs6578743	0.92[ASN][1000 genomes]
rs6578744	1.00[ASN][1000 genomes]
rs7110410	0.81[ASN][1000 genomes]
rs7117911	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7480133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs7930953	0.89[ASN][1000 genomes]
rs7944650	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948429	0.89[ASN][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	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1052156	chr11:6003428-6107778	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv1047794	chr11:6003428-6116105	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv19708	chr11:6076999-6117545	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4758380	TMEM9B	cis	parietal	SCAN
rs4758380	PPFIBP2	cis	cerebellum	SCAN
rs4758380	OVCH2	cis	parietal	SCAN
rs4758380	OR52N2	cis	parietal	SCAN
rs4758380	OR52N4	cis	parietal	SCAN
rs4758380	DNHD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:6099400-6101000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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