Variant report

Variant	rs533573
Chromosome Location	chr19:39515939-39515940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10410965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666514	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12150941	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1268240	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs1268251	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978285	0.89[ASN][1000 genomes]
rs2012598	0.83[EUR][1000 genomes]
rs2081994	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2081995	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2318895	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2318896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2873834	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2873835	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2873836	0.88[ASN][1000 genomes]
rs34640039	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4305198	0.82[EUR][1000 genomes]
rs472104	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs473729	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473878	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.83[ASN][1000 genomes]
rs476616	0.84[ASN][1000 genomes]
rs479001	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802004	0.88[ASN][1000 genomes]
rs4802012	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803179	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803180	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803184	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs485226	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497378	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs536244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580494	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs586059	0.82[ASN][1000 genomes]
rs601966	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs603268	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629685	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs631879	0.84[ASN][1000 genomes]
rs631952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646580	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs650450	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7247817	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7254745	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258182	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73047946	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103036	0.81[EUR][1000 genomes]
rs8103319	0.81[EUR][1000 genomes]
rs8105050	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109914	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs533573	LOC390940	cis	cerebellum	SCAN
rs533573	PSG3	cis	cerebellum	SCAN
rs533573	BLOC1S3	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39481000-39516000	Weak transcription	Brain Angular Gyrus	brain
2	chr19:39487200-39518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:39498400-39516600	Weak transcription	A549	lung
4	chr19:39499400-39516600	Weak transcription	Brain Anterior Caudate	brain
5	chr19:39499800-39516800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr19:39502400-39518000	Weak transcription	Aorta	Aorta
7	chr19:39503600-39520200	Weak transcription	Liver	Liver
8	chr19:39506800-39517200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:39507200-39517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:39510600-39516800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:39511200-39517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39512400-39518000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39513000-39521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:39513000-39521600	Weak transcription	Right Atrium	heart
15	chr19:39513200-39517400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:39513600-39517400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:39514000-39516200	Enhancers	K562	blood
18	chr19:39514000-39517600	Weak transcription	NHEK	skin
19	chr19:39514000-39521400	Weak transcription	Pancreas	Pancrea
20	chr19:39514000-39522200	Weak transcription	Gastric	stomach
21	chr19:39514200-39517800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:39514200-39517800	Weak transcription	Placenta	Placenta
23	chr19:39514400-39517400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:39514400-39517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:39514400-39517800	Weak transcription	Brain Germinal Matrix	brain
26	chr19:39514400-39517800	Weak transcription	Left Ventricle	heart
27	chr19:39514400-39520400	Weak transcription	Fetal Intestine Large	intestine
28	chr19:39514400-39521600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:39514400-39521800	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:39514600-39517600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:39514600-39517600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:39514600-39521400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:39514800-39517600	Weak transcription	Lung	lung
34	chr19:39514800-39518600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:39514800-39519600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:39514800-39520000	Strong transcription	Brain Cingulate Gyrus	brain
37	chr19:39515000-39517200	Enhancers	GM12878-XiMat	blood
38	chr19:39515000-39518000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:39515200-39521600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:39515400-39516800	Strong transcription	Fetal Intestine Small	intestine
41	chr19:39515400-39517400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:39515400-39519000	Strong transcription	Brain Hippocampus Middle	brain
43	chr19:39515600-39516800	Strong transcription	Esophagus	oesophagus
44	chr19:39515600-39517800	Strong transcription	Fetal Stomach	stomach
45	chr19:39515600-39518400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr19:39515600-39518600	Strong transcription	Brain Substantia Nigra	brain
47	chr19:39515600-39518800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:39515800-39517600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:39515800-39518000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:39515800-39518400	Strong transcription	Adipose Nuclei	Adipose

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