Variant report

Variant	rs11083244
Chromosome Location	chr18:25643844-25643845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11083247	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564295	0.86[CEU][hapmap]
rs11564383	1.00[YRI][hapmap]
rs11564394	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11564398	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564401	1.00[ASW][hapmap];0.95[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11564403	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564410	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564414	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11564418	0.85[CEU][hapmap]
rs11564420	1.00[YRI][hapmap]
rs11664205	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11664343	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs1220027	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12454980	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956425	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12957702	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957780	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12971156	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1550662	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468213	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17468261	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17468415	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468443	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468699	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469315	1.00[YRI][hapmap]

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	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11083244	PGA4	trans	lymphoblastoid	seeQTL
rs11083244	RIOK3	cis	parietal	SCAN
rs11083244	C18orf16	cis	parietal	SCAN
rs11083244	PGA3	trans	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25625800-25650400	Weak transcription	Right Atrium	heart
2	chr18:25627600-25645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:25641200-25645000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr18:25641400-25645000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr18:25641600-25644200	Weak transcription	Left Ventricle	heart
6	chr18:25642400-25646800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:25642400-25646800	Enhancers	HSMM	muscle
8	chr18:25642600-25644000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr18:25642600-25644000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr18:25642600-25644000	Enhancers	Brain Substantia Nigra	brain
11	chr18:25642600-25644200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr18:25642600-25645000	Enhancers	Ovary	ovary
13	chr18:25642600-25645000	Enhancers	Osteobl	bone
14	chr18:25642600-25646200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr18:25642600-25646800	Enhancers	Fetal Heart	heart
16	chr18:25642800-25644000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr18:25642800-25644000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:25642800-25644000	Enhancers	NHLF	lung
19	chr18:25642800-25644800	Enhancers	HSMMtube	muscle
20	chr18:25642800-25646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr18:25642800-25647400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr18:25643000-25645000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:25643000-25655200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:25643200-25644000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr18:25643200-25644000	Enhancers	Fetal Kidney	kidney
26	chr18:25643200-25644200	Enhancers	HUVEC	blood vessel
27	chr18:25643200-25644800	Enhancers	A549	lung
28	chr18:25643200-25645800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr18:25643200-25646000	Enhancers	Brain Hippocampus Middle	brain
30	chr18:25643200-25646600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:25643200-25646800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:25643200-25647400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr18:25643400-25644200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr18:25643400-25644200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr18:25643400-25644200	Enhancers	Fetal Lung	lung
36	chr18:25643400-25644200	Enhancers	HepG2	liver
37	chr18:25643400-25644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr18:25643600-25644000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr18:25643600-25644200	Weak transcription	Aorta	Aorta
40	chr18:25643600-25644200	Enhancers	NH-A	brain
41	chr18:25643600-25644400	Enhancers	Right Ventricle	heart
42	chr18:25643600-25644800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:25643600-25644800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr18:25643800-25644200	Weak transcription	Brain Germinal Matrix	brain
45	chr18:25643800-25644800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr18:25643800-25644800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr18:25643800-25644800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr18:25643800-25644800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr18:25643800-25644800	Weak transcription	Brain Angular Gyrus	brain
50	chr18:25643800-25644800	Weak transcription	Brain Anterior Caudate	brain

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