Variant report

Variant	rs2499936
Chromosome Location	chr11:5110068-5110069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10734476	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10837374	0.87[ASN][1000 genomes]
rs10837375	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs11035764	0.87[ASN][1000 genomes]
rs1455950	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2445256	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2445261	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2445265	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2445296	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445297	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499937	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499938	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2499943	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499944	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499945	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2500058	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs2500059	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2500060	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2959188	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3002645	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4426129	0.87[ASN][1000 genomes]
rs4517504	0.82[ASN][1000 genomes]
rs4910713	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7114854	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv553219	chr11:5026200-5214413	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv896920	chr11:5068137-5221825	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv2422503	chr11:5087292-5125991	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv1054412	chr11:5087318-5126477	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv467667	chr11:5091633-5121790	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv553220	chr11:5091633-5121790	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv896922	chr11:5091633-5121790	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv553221	chr11:5091882-5116128	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv896923	chr11:5091882-5199208	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
16	nsv896924	chr11:5098714-5221825	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	nsv553222	chr11:5102476-5151516	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2499936	MRPL23	cis	parietal	SCAN
rs2499936	NUP98	cis	cerebellum	SCAN
rs2499936	TRPC2	cis	cerebellum	SCAN
rs2499936	APH1B	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5109600-5110600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr11:5110000-5110600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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