Variant report

Variant	rs11212474
Chromosome Location	chr11:107863730-107863731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11212475	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11600706	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11600740	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11602683	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11603079	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11605419	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11605878	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11606820	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11607758	0.91[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11822270	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11822609	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11822651	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11825746	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11825936	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11828176	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17107675	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17617000	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741053	0.80[EUR][1000 genomes]
rs3781870	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs4565865	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58243661	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6588998	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7103534	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7107097	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7118335	1.00[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7125285	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7130647	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73555359	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73555372	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73555391	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73557106	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73557111	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73557122	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73557155	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73557188	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7927717	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7929383	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7936826	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7943669	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7947408	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2750980	chr11:107720941-107970986	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1043139	chr11:107725297-107869216	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1047984	chr11:107794729-107950746	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1040345	chr11:107824764-107924309	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
10	esv3415118	chr11:107844791-107881474	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11212474	MGC33948	cis	multi-tissue	Pritchard
rs11212474	ACAT1	cis	cerebellum	SCAN
rs11212474	ACAT1	cis	multi-tissue	Pritchard
rs11212474	ACAT1	cis	parietal	SCAN
rs11212474	GRIA4	cis	parietal	SCAN
rs11212474	GUCY1A2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107863600-107879400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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