Variant report

Variant	rs17618045
Chromosome Location	chr2:63793255-63793256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10496102	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs1109027	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12463603	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12464471	0.81[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs12470478	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12472865	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12476015	0.80[EUR][1000 genomes]
rs17618390	1.00[YRI][hapmap]
rs17619012	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2054120	0.82[EUR][1000 genomes]
rs2278718	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs4671062	0.80[EUR][1000 genomes]
rs72806010	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72806027	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72806056	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72821631	0.82[EUR][1000 genomes]
rs72821632	0.82[EUR][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	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17618045	GNAO1	trans	lymphoblastoid	RTeQTL
rs17618045	CCT4	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63777400-63806800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:63778800-63794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:63780200-63814800	Weak transcription	Psoas Muscle	Psoas
4	chr2:63781000-63804000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:63782600-63793400	Weak transcription	Lung	lung
6	chr2:63783400-63798600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:63783600-63793800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:63787000-63793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:63789000-63808200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:63789000-63808200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:63789400-63794200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:63789400-63796600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:63789600-63795800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:63790600-63803000	Weak transcription	Fetal Heart	heart
15	chr2:63791000-63793400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:63791400-63794600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:63791800-63798800	Weak transcription	Adipose Nuclei	Adipose
18	chr2:63793200-63794000	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr2:63793200-63794400	ZNF genes & repeats	Primary B cells from cord blood	blood
20	chr2:63793200-63794800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr2:63793200-63796800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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