Variant report

Variant	rs3824954
Chromosome Location	chr11:86153082-86153083
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	chr11:86152679..86155183-chr11:86156191..86160903,4	K562	blood:
2	chr11:86150631..86153511-chr11:86154013..86155677,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1042780	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[ASN][1000 genomes]
rs10501617	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[ASN][1000 genomes]
rs10501618	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11234640	0.85[ASN][1000 genomes]
rs11234642	0.84[CHB][hapmap];0.93[ASN][1000 genomes]
rs11234649	0.94[ASN][1000 genomes]
rs11234656	0.94[ASN][1000 genomes]
rs11607319	0.94[ASN][1000 genomes]
rs12271571	0.93[ASN][1000 genomes]
rs12272337	0.94[ASN][1000 genomes]
rs12272824	0.94[ASN][1000 genomes]
rs12274297	0.94[ASN][1000 genomes]
rs12289721	0.94[ASN][1000 genomes]
rs1452133	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452135	0.94[ASN][1000 genomes]
rs1452138	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597792	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1839940	0.94[ASN][1000 genomes]
rs2034622	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436284	0.93[ASN][1000 genomes]
rs3741006	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs3741007	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3819227	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4586193	0.94[ASN][1000 genomes]
rs4943940	0.93[ASN][1000 genomes]
rs4944572	0.89[CEU][hapmap];0.93[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4944573	0.94[ASN][1000 genomes]
rs4944574	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs4944578	0.92[ASN][1000 genomes]
rs59419027	0.94[ASN][1000 genomes]
rs6592293	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120275	0.92[ASN][1000 genomes]
rs7926796	0.94[ASN][1000 genomes]
rs7930223	0.94[ASN][1000 genomes]
rs7932498	0.93[ASN][1000 genomes]
rs7932514	0.91[ASN][1000 genomes]
rs7937668	0.93[ASN][1000 genomes]
rs7947323	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947537	0.94[ASN][1000 genomes]
rs7949910	0.94[ASN][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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3824954	NOX4	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86136800-86170200	Weak transcription	Fetal Heart	heart
2	chr11:86138600-86167400	Weak transcription	Fetal Lung	lung
3	chr11:86140800-86153400	Weak transcription	Right Ventricle	heart
4	chr11:86140800-86155800	Weak transcription	Psoas Muscle	Psoas
5	chr11:86141000-86153400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:86142000-86153600	Weak transcription	Brain Angular Gyrus	brain
7	chr11:86142000-86167400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:86142600-86153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:86142600-86155000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:86142600-86156000	Weak transcription	Spleen	Spleen
11	chr11:86142800-86157600	Weak transcription	Gastric	stomach
12	chr11:86143000-86153400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:86143600-86153600	Weak transcription	Fetal Intestine Small	intestine
14	chr11:86145200-86153200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:86145400-86167400	Weak transcription	Pancreas	Pancrea
16	chr11:86147200-86153600	Weak transcription	Aorta	Aorta
17	chr11:86147200-86153800	Weak transcription	Lung	lung
18	chr11:86148200-86154600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:86149200-86154400	Weak transcription	Fetal Intestine Large	intestine
20	chr11:86149400-86154800	Enhancers	NHDF-Ad	bronchial
21	chr11:86149800-86158600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:86150200-86156200	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:86150200-86158400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:86150200-86167400	Weak transcription	Stomach Mucosa	stomach
25	chr11:86150400-86153400	Weak transcription	A549	lung
26	chr11:86150600-86155000	Strong transcription	Ovary	ovary
27	chr11:86150600-86159400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:86150800-86153800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:86150800-86154200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:86151000-86154000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:86151000-86154200	Enhancers	NHLF	lung
32	chr11:86151000-86155000	Strong transcription	Left Ventricle	heart
33	chr11:86151000-86159200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:86151200-86153600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:86151200-86158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:86151200-86159800	Strong transcription	Fetal Brain Female	brain
37	chr11:86151200-86159800	Strong transcription	Fetal Stomach	stomach
38	chr11:86151400-86153600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:86151400-86153800	Weak transcription	Right Atrium	heart
40	chr11:86151400-86158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:86151600-86154200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:86151800-86153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:86151800-86153400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:86151800-86153400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr11:86151800-86154800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:86151800-86167400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:86151800-86167400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:86152000-86153800	Enhancers	Osteobl	bone
49	chr11:86152000-86154800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:86152000-86155000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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