Variant report

Variant	rs8182472
Chromosome Location	chr19:19539891-19539892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19514824..19526614-chr19:19535593..19543548,15	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10408596	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10408875	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10424702	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10500212	0.83[JPT][hapmap]
rs11668104	1.00[CEU][hapmap]
rs11668386	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672355	0.80[EUR][1000 genomes]
rs12052117	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12610185	0.83[JPT][hapmap]
rs16996148	0.83[JPT][hapmap]
rs16996185	0.82[JPT][hapmap]
rs17216525	0.83[JPT][hapmap]
rs17216588	0.83[JPT][hapmap]
rs28720066	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2965185	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs3794991	0.92[JPT][hapmap]
rs56241616	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56273306	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56397647	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57009615	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59148799	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73002960	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8182472	ATP13A1	cis	multi-tissue	Pritchard
rs8182472	KIAA0892	cis	multi-tissue	Pritchard
rs8182472	ATP13A1	cis	brain	seeQTL
rs8182472	EPS15L1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19518600-19549800	Weak transcription	Fetal Brain Female	brain
2	chr19:19520800-19546800	Weak transcription	Hela-S3	cervix
3	chr19:19521000-19545400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:19522000-19545000	Weak transcription	Fetal Lung	lung
5	chr19:19522200-19548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:19528800-19544200	Weak transcription	Fetal Heart	heart
8	chr19:19530000-19545400	Weak transcription	Colonic Mucosa	Colon
9	chr19:19530200-19543400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:19530200-19547400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:19531400-19541600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:19531400-19545000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:19532200-19541400	Weak transcription	Small Intestine	intestine
14	chr19:19532400-19540000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:19532400-19543400	Weak transcription	Primary T cells from cord blood	blood
16	chr19:19532400-19544400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr19:19532400-19545000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:19533200-19544000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:19533400-19543600	Weak transcription	Ovary	ovary
20	chr19:19534400-19540000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:19534800-19543800	Weak transcription	K562	blood
22	chr19:19534800-19548400	Weak transcription	HSMM	muscle
23	chr19:19535000-19544800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:19535000-19545000	Weak transcription	Osteobl	bone
25	chr19:19535400-19542200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:19536200-19545200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr19:19536800-19545000	Weak transcription	Aorta	Aorta
28	chr19:19536800-19545200	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:19536800-19545400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:19536800-19545400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:19537000-19544800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:19537000-19545000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:19537000-19546800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:19537000-19549000	Weak transcription	Brain Germinal Matrix	brain
35	chr19:19537200-19542000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:19537200-19542000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr19:19537200-19549200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr19:19537400-19540800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:19537400-19541600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:19537600-19540000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr19:19537600-19542200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:19537800-19544000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:19537800-19549800	Weak transcription	A549	lung
44	chr19:19538000-19541400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:19538000-19542200	Strong transcription	Dnd41	blood
46	chr19:19538000-19543400	Weak transcription	Liver	Liver
47	chr19:19538000-19544200	Weak transcription	HUVEC	blood vessel
48	chr19:19538000-19546800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:19538200-19540200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr19:19538200-19543800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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