Variant report

Variant	rs12294533
Chromosome Location	chr11:72684898-72684899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:72682058..72684979-chr11:72694471..72696981,2	MCF-7	breast:
2	chr11:72681582..72683189-chr11:72684693..72686760,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10437750	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793048	0.86[YRI][hapmap]
rs10793049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs10793054	0.95[YRI][hapmap]
rs10793055	0.85[ASW][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10793056	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10898881	0.82[YRI][hapmap]
rs10898885	0.86[YRI][hapmap]
rs10898894	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898895	0.91[CHB][hapmap];0.95[YRI][hapmap]
rs10898896	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10898900	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235612	0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs11235651	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12288580	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12289752	0.83[ASN][1000 genomes]
rs12293726	0.84[ASN][1000 genomes]
rs1982585	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187494	0.82[YRI][hapmap]
rs2276379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303969	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs4394861	0.86[YRI][hapmap]
rs4944816	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55671951	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60355221	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6592500	0.86[YRI][hapmap]
rs6592508	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7104158	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925928	0.95[YRI][hapmap]
rs7936751	0.95[YRI][hapmap]
rs7937701	0.96[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7943424	0.80[ASW][hapmap];0.89[GIH][hapmap];0.91[YRI][hapmap]
rs9645708	0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv555411	chr11:72647296-72800970	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12294533	ATG16L2	cis	parietal	SCAN
rs12294533	KRTAP5-11	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72636200-72694800	Weak transcription	Adipose Nuclei	Adipose
2	chr11:72636400-72712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr11:72637000-72721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:72649000-72721600	Weak transcription	Thymus	Thymus
5	chr11:72651400-72696600	Weak transcription	Brain Anterior Caudate	brain
6	chr11:72666200-72689600	Weak transcription	Esophagus	oesophagus
7	chr11:72666600-72721600	Weak transcription	Lung	lung
8	chr11:72667000-72700600	Weak transcription	Brain Angular Gyrus	brain
9	chr11:72669400-72689600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:72669800-72721800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:72671000-72689400	Weak transcription	Fetal Lung	lung
12	chr11:72671200-72687400	Weak transcription	Fetal Brain Female	brain
13	chr11:72673000-72708000	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:72674600-72687200	Weak transcription	Placenta	Placenta
15	chr11:72675000-72687400	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:72675000-72692000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:72675000-72692800	Weak transcription	HepG2	liver
18	chr11:72675200-72700600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:72675600-72687200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:72675600-72696600	Weak transcription	Brain Substantia Nigra	brain
21	chr11:72675600-72696800	Weak transcription	Fetal Kidney	kidney
22	chr11:72675800-72690600	Weak transcription	Liver	Liver
23	chr11:72675800-72700800	Weak transcription	Spleen	Spleen
24	chr11:72679400-72687600	Enhancers	NHDF-Ad	bronchial
25	chr11:72679600-72687600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:72680200-72687600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr11:72680200-72689600	Weak transcription	Fetal Thymus	thymus
28	chr11:72680600-72687800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:72681000-72685800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr11:72681200-72685400	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:72681400-72690400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:72681800-72689400	Weak transcription	HUVEC	blood vessel
33	chr11:72681800-72720200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:72682000-72686600	Weak transcription	NHEK	skin
35	chr11:72682000-72687200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:72682000-72687200	Weak transcription	HMEC	breast
37	chr11:72682000-72689400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:72682000-72690200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:72682000-72695000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:72682000-72695600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:72682000-72701400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:72682000-72710600	Weak transcription	Aorta	Aorta
43	chr11:72682200-72686800	Weak transcription	NH-A	brain
44	chr11:72682200-72695200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:72682200-72696600	Weak transcription	Colonic Mucosa	Colon
46	chr11:72682600-72696600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:72682800-72685200	Weak transcription	Ovary	ovary
48	chr11:72682800-72686000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:72682800-72686400	Weak transcription	Hela-S3	cervix
50	chr11:72682800-72687400	Weak transcription	Right Atrium	heart

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