Variant report

Variant	rs7273889
Chromosome Location	chr20:1252492-1252493
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	chr20:1246074..1249066-chr20:1250253..1252765,2	K562	blood:

Variant related genes	Relation type
ENSG00000101298	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10485821	0.87[GIH][hapmap]
rs10485822	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs1407766	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17717241	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs17779421	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs17779586	0.87[GIH][hapmap]
rs4813073	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs4814030	0.89[ASN][1000 genomes]
rs4814031	0.89[ASN][1000 genomes]
rs6040984	1.00[ASN][1000 genomes]
rs60609218	0.89[ASN][1000 genomes]
rs7265362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7266780	0.94[GIH][hapmap]
rs7271372	0.87[GIH][hapmap]
rs73890804	0.89[ASN][1000 genomes]
rs73890806	0.89[ASN][1000 genomes]
rs8122738	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7273889	PANK2	cis	cerebellum	SCAN
rs7273889	SMOX	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1247600-1253200	Weak transcription	Aorta	Aorta
2	chr20:1247800-1261000	Weak transcription	Right Ventricle	heart
3	chr20:1247800-1262000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:1248000-1252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr20:1248000-1253200	Weak transcription	Lung	lung
6	chr20:1248000-1253200	Weak transcription	HSMM	muscle
7	chr20:1248000-1253400	Weak transcription	Brain Germinal Matrix	brain
8	chr20:1248000-1253600	Weak transcription	NHDF-Ad	bronchial
9	chr20:1248000-1255800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr20:1248000-1260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:1248000-1260800	Weak transcription	Osteobl	bone
12	chr20:1248000-1266800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:1248000-1271800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:1248000-1278600	Weak transcription	Spleen	Spleen
15	chr20:1248200-1252600	Weak transcription	HSMMtube	muscle
16	chr20:1248200-1252800	Weak transcription	Fetal Muscle Leg	muscle
17	chr20:1248200-1253400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr20:1248200-1253400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr20:1248200-1253400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:1248200-1255200	Weak transcription	Fetal Brain Female	brain
21	chr20:1248200-1255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:1248200-1260400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr20:1248200-1260600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr20:1248200-1265000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr20:1248200-1277400	Weak transcription	Fetal Stomach	stomach
26	chr20:1248200-1281200	Weak transcription	NHEK	skin
27	chr20:1248400-1253000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:1248400-1253400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr20:1248400-1255600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr20:1248400-1261400	Weak transcription	Colon Smooth Muscle	Colon
31	chr20:1248600-1253600	Weak transcription	Brain Hippocampus Middle	brain
32	chr20:1248600-1266800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr20:1248800-1253200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr20:1248800-1253400	Weak transcription	Gastric	stomach
35	chr20:1248800-1258000	Weak transcription	NHLF	lung
36	chr20:1248800-1263600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr20:1249000-1255400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr20:1249000-1281400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr20:1249800-1253000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr20:1249800-1258000	Weak transcription	Pancreas	Pancrea
41	chr20:1249800-1262200	Weak transcription	Left Ventricle	heart
42	chr20:1250200-1253000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr20:1250400-1253000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr20:1250800-1255200	Weak transcription	Brain Angular Gyrus	brain
45	chr20:1251400-1255200	Weak transcription	K562	blood
46	chr20:1251400-1255400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr20:1251800-1252800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr20:1251800-1253000	Weak transcription	Brain Anterior Caudate	brain
49	chr20:1251800-1253800	Weak transcription	Primary T cells from cord blood	blood
50	chr20:1251800-1254000	Enhancers	Primary T helper cells fromperipheralblood	blood

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