Variant report

Variant	rs2653556
Chromosome Location	chr11:8906636-8906637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1025438	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10734639	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs10769974	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs10769977	0.87[CEU][hapmap]
rs10840151	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs10840154	0.87[CEU][hapmap]
rs10840156	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs12798311	0.84[EUR][1000 genomes]
rs2016844	0.96[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2056903	0.84[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2116510	0.87[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs2116511	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2163625	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap]
rs2246878	0.83[EUR][1000 genomes]
rs2247038	0.83[EUR][1000 genomes]
rs2568029	0.82[MEX][hapmap]
rs2568034	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568042	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568069	0.87[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2568074	0.83[EUR][1000 genomes]
rs2568075	0.83[EUR][1000 genomes]
rs2568077	0.83[EUR][1000 genomes]
rs2568079	0.95[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2568081	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2653560	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2653562	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2653565	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653601	0.96[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2653604	0.87[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs2653611	0.81[EUR][1000 genomes]
rs2742487	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2742488	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2742491	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2742493	0.91[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs2742495	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs2742496	0.96[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2742497	0.96[CEU][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2742504	0.81[EUR][1000 genomes]
rs2742505	0.81[EUR][1000 genomes]
rs2742512	0.83[EUR][1000 genomes]
rs2742513	0.83[EUR][1000 genomes]
rs2742514	0.87[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs2742519	0.87[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2742520	0.91[EUR][1000 genomes]
rs2742521	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751063	0.96[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs3751066	0.87[CEU][hapmap]
rs3751068	0.87[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs3763911	0.91[CEU][hapmap]
rs3763912	0.91[CEU][hapmap];0.87[GIH][hapmap]
rs4909951	0.96[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs4910068	0.82[LWK][hapmap]
rs6486061	0.82[MEX][hapmap]
rs7106539	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs909464	0.83[EUR][1000 genomes]
rs9300096	0.96[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs982273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2653556	C11orf17	cis	cerebellum	SCAN
rs2653556	OR52E6	cis	parietal	SCAN
rs2653556	C11orf17	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8901000-8908000	Weak transcription	Psoas Muscle	Psoas
2	chr11:8904000-8908000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:8906400-8907200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr11:8906400-8907600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:8906600-8906800	Enhancers	Spleen	Spleen

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