Variant report

Variant	rs2017988
Chromosome Location	chr18:8359407-8359408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11873699	0.87[YRI][hapmap]
rs11877672	0.87[YRI][hapmap]
rs1459173	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17490458	0.87[YRI][hapmap]
rs17490807	0.87[YRI][hapmap]
rs17490828	0.87[YRI][hapmap]
rs2017965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242148	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7244164	0.87[YRI][hapmap]
rs8087223	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv3351324	chr18:8250514-8405140	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1058445	chr18:8270681-8421249	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2017988	C18orf18	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8329800-8365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:8340200-8365600	Weak transcription	Psoas Muscle	Psoas
3	chr18:8342000-8362400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr18:8342200-8359600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr18:8342200-8366800	Weak transcription	Adipose Nuclei	Adipose
6	chr18:8342200-8367400	Weak transcription	Aorta	Aorta
7	chr18:8342600-8366400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr18:8344200-8367000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:8346400-8366800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr18:8350200-8362000	Weak transcription	Lung	lung
11	chr18:8350200-8366200	Weak transcription	Pancreas	Pancrea
12	chr18:8350200-8367200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr18:8350400-8359800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr18:8352400-8367200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr18:8352600-8372600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:8354800-8366800	Weak transcription	HSMMtube	muscle
17	chr18:8355200-8378200	Weak transcription	Gastric	stomach
18	chr18:8355400-8363200	Weak transcription	Fetal Heart	heart
19	chr18:8355400-8364800	Weak transcription	Left Ventricle	heart
20	chr18:8356400-8361000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr18:8356400-8365600	Weak transcription	Right Ventricle	heart
22	chr18:8356600-8359800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr18:8357600-8359600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr18:8357800-8366800	Weak transcription	Spleen	Spleen
25	chr18:8358200-8359800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr18:8358200-8360800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr18:8358400-8362600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr18:8358400-8378200	Weak transcription	HepG2	liver
29	chr18:8358600-8359600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr18:8358600-8363000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr18:8358800-8364400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr18:8358800-8365200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr18:8358800-8365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr18:8358800-8366800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:8359200-8359600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr18:8359200-8359800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:8359200-8360000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:8359200-8360000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:8359400-8359600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:8359400-8359800	Enhancers	Right Atrium	heart
41	chr18:8359400-8360000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr18:8359400-8360600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr18:8359400-8362400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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