Variant report

Variant	rs1494373
Chromosome Location	chr1:220929356-220929357
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	chr1:220926710..220928570-chr1:220929149..220931113,2	MCF-7	breast:
2	chr1:220920532..220923272-chr1:220926936..220929369,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11589296	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11809755	0.85[EUR][1000 genomes]
rs12407624	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17008587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337163	0.91[EUR][1000 genomes]
rs337166	0.85[EUR][1000 genomes]
rs337167	0.85[EUR][1000 genomes]
rs337168	0.85[EUR][1000 genomes]
rs337174	0.84[EUR][1000 genomes]
rs337182	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs337188	0.95[EUR][1000 genomes]
rs337192	0.91[EUR][1000 genomes]
rs365346	0.80[TSI][hapmap]
rs3753878	0.86[EUR][1000 genomes]
rs3753879	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41314538	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59423796	0.91[EUR][1000 genomes]
rs61830238	0.91[EUR][1000 genomes]
rs61830262	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6659246	0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs774139	0.89[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Response to antipsychotic therapy (extrapyramidal side effects)	19875103	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1494373	C1orf115	cis	multi-tissue	Pritchard
rs1494373	MOSC2	cis	cerebellum	SCAN
rs1494373	TGFB2	cis	cerebellum	SCAN
rs1494373	EPRS	cis	cerebellum	SCAN
rs1494373	C1orf115	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922400-220932200	Weak transcription	HSMMtube	muscle
2	chr1:220922600-220929400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:220922600-220929400	Weak transcription	Esophagus	oesophagus
4	chr1:220922600-220931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:220923200-220930400	Weak transcription	Spleen	Spleen
10	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:220924200-220931000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:220924200-220936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:220924600-220936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:220924600-220944000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:220924800-220931200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:220924800-220945600	Weak transcription	Osteobl	bone
17	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:220925200-220942000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:220925200-220943400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:220925800-220931800	Strong transcription	Fetal Intestine Small	intestine
23	chr1:220925800-220938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:220927000-220933000	Weak transcription	Right Ventricle	heart
25	chr1:220927200-220933200	Weak transcription	Small Intestine	intestine
26	chr1:220927400-220929800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:220927400-220930400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr1:220927600-220930800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:220927600-220931200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:220927600-220931200	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:220927600-220931200	Strong transcription	Hela-S3	cervix
32	chr1:220927600-220934400	Weak transcription	Stomach Mucosa	stomach
33	chr1:220927800-220929400	Weak transcription	NHLF	lung
34	chr1:220927800-220929600	Strong transcription	HepG2	liver
35	chr1:220927800-220930800	Strong transcription	Gastric	stomach
36	chr1:220927800-220931000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:220927800-220931000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:220927800-220931200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:220927800-220931200	Strong transcription	Fetal Intestine Large	intestine
40	chr1:220927800-220931200	Strong transcription	Pancreas	Pancrea
41	chr1:220927800-220931400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:220927800-220931600	Strong transcription	Lung	lung
43	chr1:220927800-220938600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:220928000-220930200	Strong transcription	Colonic Mucosa	Colon
45	chr1:220928000-220931000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:220928000-220931200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:220928000-220931200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:220928000-220931200	Strong transcription	Ovary	ovary
49	chr1:220928000-220931200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:220928000-220933600	Strong transcription	Fetal Stomach	stomach

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