Variant report

Variant	rs7936751
Chromosome Location	chr11:72720199-72720200
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10793048	0.82[YRI][hapmap]
rs10793049	0.86[YRI][hapmap]
rs10793054	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10793055	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793056	0.86[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[YRI][hapmap]
rs10898885	0.82[YRI][hapmap]
rs10898894	0.95[YRI][hapmap]
rs10898895	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11235612	1.00[ASW][hapmap];0.87[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap]
rs1126205	0.84[ASW][hapmap]
rs12294533	0.95[YRI][hapmap]
rs2276379	0.95[YRI][hapmap]
rs2303969	0.82[CEU][hapmap];0.95[YRI][hapmap]
rs4394861	0.82[YRI][hapmap]
rs6592500	0.82[YRI][hapmap]
rs6592508	0.86[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[YRI][hapmap]
rs7129921	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7925466	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925928	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7937701	0.86[CHB][hapmap];0.95[YRI][hapmap]
rs7943424	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[YRI][hapmap]
rs9645708	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7936751	NOG	trans	cerebellum	SCAN
rs7936751	KRTAP5-11	cis	cerebellum	SCAN
rs7936751	ATG16L2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72637000-72721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:72649000-72721600	Weak transcription	Thymus	Thymus
3	chr11:72666600-72721600	Weak transcription	Lung	lung
4	chr11:72669800-72721800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:72681800-72720200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:72682800-72721600	Weak transcription	Right Ventricle	heart
7	chr11:72684000-72721600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:72686600-72721600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:72687600-72722200	Weak transcription	NHLF	lung
10	chr11:72687600-72724200	Weak transcription	HMEC	breast
11	chr11:72688600-72721600	Weak transcription	Brain Germinal Matrix	brain
12	chr11:72693400-72721600	Weak transcription	Left Ventricle	heart
13	chr11:72695600-72720400	Weak transcription	Adipose Nuclei	Adipose
14	chr11:72696000-72720200	Weak transcription	Fetal Intestine Large	intestine
15	chr11:72696000-72720800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:72696000-72724000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:72697000-72721600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:72697200-72720600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:72699200-72721600	Weak transcription	HSMM	muscle
20	chr11:72699600-72720200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr11:72700000-72720800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:72700600-72720600	Weak transcription	Fetal Brain Male	brain
23	chr11:72700800-72720400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:72701000-72720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:72701000-72721600	Weak transcription	Pancreas	Pancrea
26	chr11:72701000-72727200	Weak transcription	HUVEC	blood vessel
27	chr11:72701200-72721600	Weak transcription	Ovary	ovary
28	chr11:72705400-72721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:72705600-72720600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:72705600-72721000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr11:72708200-72720400	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:72708400-72720600	Weak transcription	Brain Substantia Nigra	brain
33	chr11:72708400-72721600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:72708600-72720600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:72709000-72720800	Weak transcription	Liver	Liver
36	chr11:72711000-72721600	Weak transcription	Aorta	Aorta
37	chr11:72711200-72720200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr11:72711200-72721600	Weak transcription	Osteobl	bone
39	chr11:72711200-72723000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:72712600-72720200	Weak transcription	Fetal Thymus	thymus
41	chr11:72713000-72720600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:72713400-72720600	Weak transcription	A549	lung
43	chr11:72713400-72721400	Weak transcription	Fetal Lung	lung
44	chr11:72714400-72720600	Weak transcription	Dnd41	blood
45	chr11:72715000-72723000	ZNF genes & repeats	GM12878-XiMat	blood
46	chr11:72716200-72720600	Strong transcription	Primary B cells from cord blood	blood
47	chr11:72716200-72731200	Weak transcription	Fetal Kidney	kidney
48	chr11:72716600-72721600	Weak transcription	Spleen	Spleen
49	chr11:72717200-72720400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:72717600-72721600	Weak transcription	Gastric	stomach

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