Variant report

Variant	rs10832890
Chromosome Location	chr11:18172814-18172815
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1001139	0.82[ASN][1000 genomes]
rs10766458	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832889	0.86[ASN][1000 genomes]
rs10832893	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024502	0.84[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024530	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024531	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024539	0.84[ASW][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1350098	0.81[ASN][1000 genomes]
rs1378607	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs1378608	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs1378611	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs1378612	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs1531104	0.83[CHB][hapmap]
rs1531105	0.83[CHB][hapmap]
rs1902266	0.85[JPT][hapmap]
rs1968730	0.83[CHB][hapmap]
rs1968732	0.83[CHB][hapmap]
rs2014694	0.83[CHB][hapmap]
rs2078066	0.83[CHB][hapmap]
rs2124375	0.83[CHB][hapmap]
rs2124376	0.83[CHB][hapmap]
rs2124377	0.83[CHB][hapmap]
rs2246304	0.82[CHB][hapmap]
rs2246305	0.83[CHB][hapmap]
rs2246388	0.82[CHB][hapmap]
rs2253938	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2403247	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2403248	0.83[CHB][hapmap]
rs2445164	0.89[CHB][hapmap]
rs2445165	0.91[CHB][hapmap]
rs2445182	0.83[CHB][hapmap]
rs2445183	0.83[CHB][hapmap]
rs2445196	0.81[ASN][1000 genomes]
rs2445205	0.83[CHB][hapmap]
rs2445206	0.83[CHB][hapmap]
rs2468824	0.91[CHB][hapmap]
rs2468825	0.91[CHB][hapmap]
rs2860276	0.83[CHB][hapmap]
rs2860278	0.83[CHB][hapmap]
rs4256954	0.86[ASN][1000 genomes]
rs4300374	0.86[ASN][1000 genomes]
rs4417246	0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]

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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	esv11709	chr11:18138662-18200717	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3509521	chr11:18159957-18188401	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3509522	chr11:18159957-18188401	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3367251	chr11:18159957-18196082	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv518373	chr11:18164687-18195348	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv975090	chr11:18164912-18189697	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv16635	chr11:18165268-18194893	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2762898	chr11:18166780-18198880	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1038257	chr11:18169410-18198309	Enhancers Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10832890	LDHAL6A	cis	parietal	SCAN
rs10832890	SLC6A5	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18172400-18173600	Enhancers	H1 Cell Line	embryonic stem cell
2	chr11:18172600-18173400	Enhancers	H9 Cell Line	embryonic stem cell
3	chr11:18172800-18174200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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