Variant report

Variant	rs1407766
Chromosome Location	chr20:1248286-1248287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1204614..1208313-chr20:1245857..1250887,4	K562	blood:

Variant related genes	Relation type
ENSG00000244588	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10485822	1.00[CHB][hapmap]
rs17717241	1.00[CHB][hapmap]
rs17779421	1.00[CHB][hapmap]
rs4813073	1.00[CHB][hapmap]
rs6040984	0.82[ASN][1000 genomes]
rs7265362	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7273889	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv912586	chr20:1195784-1248286	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv518957	chr20:1195784-1250463	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv912587	chr20:1205886-1248286	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1067360	chr20:1245753-1283508	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1407766	SMOX	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1246400-1248400	Active TSS	Brain Angular Gyrus	brain
2	chr20:1246400-1248600	Active TSS	Brain Cingulate Gyrus	brain
3	chr20:1246400-1248600	Active TSS	Brain Hippocampus Middle	brain
4	chr20:1246400-1249600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr20:1246600-1249000	Active TSS	Brain Anterior Caudate	brain
6	chr20:1247600-1248400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr20:1247600-1248400	Bivalent Enhancer	Placenta	Placenta
8	chr20:1247600-1248600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr20:1247600-1248800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:1247600-1249400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr20:1247600-1253200	Weak transcription	Aorta	Aorta
12	chr20:1247800-1248400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr20:1247800-1248400	Enhancers	Adipose Nuclei	Adipose
14	chr20:1247800-1248400	Enhancers	Colon Smooth Muscle	Colon
15	chr20:1247800-1248600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:1247800-1248800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr20:1247800-1248800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:1247800-1249000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr20:1247800-1249000	Enhancers	Stomach Mucosa	stomach
20	chr20:1247800-1249200	Enhancers	Left Ventricle	heart
21	chr20:1247800-1261000	Weak transcription	Right Ventricle	heart
22	chr20:1247800-1262000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr20:1248000-1248400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr20:1248000-1248400	Enhancers	Primary T cells from cord blood	blood
25	chr20:1248000-1248400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr20:1248000-1248400	Enhancers	Rectal Smooth Muscle	rectum
27	chr20:1248000-1248400	Enhancers	A549	lung
28	chr20:1248000-1248600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr20:1248000-1248600	Weak transcription	Gastric	stomach
30	chr20:1248000-1248800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr20:1248000-1248800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr20:1248000-1249000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr20:1248000-1249000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr20:1248000-1249600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr20:1248000-1251400	Enhancers	K562	blood
36	chr20:1248000-1252200	Weak transcription	Ovary	ovary
37	chr20:1248000-1252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr20:1248000-1253200	Weak transcription	Lung	lung
39	chr20:1248000-1253200	Weak transcription	HSMM	muscle
40	chr20:1248000-1253400	Weak transcription	Brain Germinal Matrix	brain
41	chr20:1248000-1253600	Weak transcription	NHDF-Ad	bronchial
42	chr20:1248000-1255800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr20:1248000-1260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr20:1248000-1260800	Weak transcription	Osteobl	bone
45	chr20:1248000-1266800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr20:1248000-1271800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:1248000-1278600	Weak transcription	Spleen	Spleen
48	chr20:1248200-1248400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr20:1248200-1248400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:1248200-1248600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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