Variant report

Variant	rs11023944
Chromosome Location	chr11:16460908-16460909
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16460793..16462936-chr11:16464207..16467731,4	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1018143	0.87[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10766320	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10766321	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10766322	0.82[ASN][1000 genomes]
rs10766323	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832598	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832599	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10832600	0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10832605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832606	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10832608	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11023945	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11820804	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12277548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12800228	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1503447	0.97[ASN][1000 genomes]
rs1503448	0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1503449	0.83[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1875717	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1910406	0.97[ASN][1000 genomes]
rs1910407	0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2089050	0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2134609	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2174162	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2174163	0.87[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs297324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs297326	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs297333	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297334	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs297339	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61881798	0.95[ASN][1000 genomes]
rs626927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7121140	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7925322	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7929425	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7929629	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7932314	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7942989	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7945277	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7951214	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs957476	0.97[ASN][1000 genomes]
rs9665965	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv897016	chr11:16455794-16691743	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11023944	LDHAL6A	cis	cerebellum	SCAN
rs11023944	C11orf58	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16452800-16461400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:16453800-16461200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:16459400-16461400	Weak transcription	Fetal Heart	heart
4	chr11:16460800-16461400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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