Variant report

Variant	rs6554109
Chromosome Location	chr4:54352035-54352036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10008334	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014056	0.81[MEX][hapmap]
rs10517296	0.81[MEX][hapmap]
rs11133267	0.81[MEX][hapmap]
rs11725230	0.81[GIH][hapmap]
rs11734039	0.81[GIH][hapmap]
rs11737139	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11944047	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12507739	0.81[GIH][hapmap]
rs12642437	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13117240	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13119372	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399241	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2128103	0.81[MEX][hapmap]
rs2412489	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28404076	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35225781	0.81[MEX][hapmap]
rs3811785	0.81[GIH][hapmap]
rs3946758	0.81[EUR][1000 genomes]
rs4864760	0.81[GIH][hapmap]
rs4864766	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59585683	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6420001	0.81[MEX][hapmap]
rs6554105	0.81[GIH][hapmap]
rs6554107	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554108	0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs6810557	0.94[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6828559	0.81[GIH][hapmap]
rs6834099	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6835629	0.91[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7682199	0.81[GIH][hapmap]
rs931181	0.81[GIH][hapmap]
rs9312639	0.81[GIH][hapmap]
rs9992820	0.81[MEX][hapmap]
rs9997844	0.81[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6554109	EXOC1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54320000-54353200	Weak transcription	Gastric	stomach
2	chr4:54327800-54362200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:54328200-54362000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:54328400-54362000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
6	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
7	chr4:54333000-54363600	Weak transcription	Aorta	Aorta
8	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:54342800-54360600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
11	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:54343400-54352200	Weak transcription	Esophagus	oesophagus
13	chr4:54343400-54363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:54343600-54352600	Weak transcription	Placenta	Placenta
15	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:54345600-54352200	Weak transcription	Fetal Intestine Small	intestine
17	chr4:54345800-54355400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:54346000-54356400	Weak transcription	HSMMtube	muscle
19	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
20	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:54347800-54355000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:54348000-54353400	Weak transcription	Pancreas	Pancrea
23	chr4:54348000-54355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:54348000-54362200	Weak transcription	Fetal Intestine Large	intestine
25	chr4:54348200-54359600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:54349000-54360000	Weak transcription	Liver	Liver
27	chr4:54349600-54352200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:54349800-54352200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:54350000-54353400	Enhancers	Ovary	ovary
30	chr4:54350400-54355200	Weak transcription	HMEC	breast
31	chr4:54350800-54352200	Enhancers	Fetal Stomach	stomach
32	chr4:54351400-54355000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:54351600-54353000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:54351600-54355000	Weak transcription	Osteobl	bone
35	chr4:54352000-54352400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:54352000-54355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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