Variant report

Variant	rs7593080
Chromosome Location	chr2:86145787-86145788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1135603	0.81[EUR][1000 genomes]
rs12616165	0.87[ASN][1000 genomes]
rs1401384	0.80[EUR][1000 genomes]
rs1438156	0.87[ASN][1000 genomes]
rs1518983	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1543972	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17026750	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1878898	1.00[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs1878904	1.00[CEU][hapmap]
rs2008559	0.87[ASN][1000 genomes]
rs2164878	0.87[ASN][1000 genomes]
rs2577768	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2577769	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2577775	0.81[EUR][1000 genomes]
rs2577777	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577778	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577779	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577780	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577786	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2679710	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2679711	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2679712	1.00[CEU][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2679713	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2679720	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2679721	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2679722	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2679725	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2918014	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2918015	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2918016	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945823	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945824	0.87[ASN][1000 genomes]
rs2945825	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945826	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35153287	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4832016	0.89[CEU][hapmap]
rs4832210	0.89[CEU][hapmap]
rs4832217	1.00[CEU][hapmap]
rs4832218	0.80[EUR][1000 genomes]
rs6547636	0.89[CEU][hapmap]
rs6547647	0.87[ASN][1000 genomes]
rs6718537	0.81[ASN][1000 genomes]
rs6720161	0.89[CEU][hapmap]
rs6734115	0.80[EUR][1000 genomes]
rs6735629	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6747179	0.80[EUR][1000 genomes]
rs6747294	0.80[EUR][1000 genomes]
rs6750686	0.87[CEU][hapmap]
rs7576135	0.85[ASN][1000 genomes]
rs764471	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs954176	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs959313	1.00[CEU][hapmap];0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7593080	PTCD3	cis	cerebellum	SCAN
rs7593080	IMMT	cis	cerebellum	SCAN
rs7593080	ST3GAL5	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86133200-86149200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:86133200-86152000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:86134400-86148000	Weak transcription	Thymus	Thymus
4	chr2:86135400-86148000	Weak transcription	Pancreas	Pancrea
5	chr2:86135400-86151600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:86135400-86151600	Weak transcription	Lung	lung
7	chr2:86135400-86152600	Weak transcription	Psoas Muscle	Psoas
8	chr2:86138200-86151600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:86138600-86147400	Weak transcription	Fetal Thymus	thymus
10	chr2:86140000-86148000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:86142000-86147200	Weak transcription	Adipose Nuclei	Adipose
12	chr2:86142200-86155800	Weak transcription	Primary T cells from cord blood	blood
13	chr2:86142400-86148000	Weak transcription	K562	blood
14	chr2:86142400-86151800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:86142400-86157800	Weak transcription	Aorta	Aorta
16	chr2:86142600-86147400	Weak transcription	Liver	Liver
17	chr2:86142600-86151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:86142600-86151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:86143200-86146800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:86143200-86148200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:86143200-86148200	Weak transcription	Brain Angular Gyrus	brain
22	chr2:86143200-86148400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:86143200-86150800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:86143400-86147800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:86143400-86148000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:86143400-86148200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:86143400-86148200	Weak transcription	Ovary	ovary
28	chr2:86143400-86148400	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:86143600-86145800	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:86143600-86147800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:86143600-86148000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:86143600-86148000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:86144800-86145800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:86145000-86146000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:86145000-86146000	Enhancers	Hela-S3	cervix
36	chr2:86145200-86145800	Enhancers	NHDF-Ad	bronchial
37	chr2:86145200-86148200	Weak transcription	Stomach Mucosa	stomach
38	chr2:86145600-86147800	Weak transcription	A549	lung
39	chr2:86145600-86151000	Weak transcription	HMEC	breast

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