Variant report

Variant	rs481103
Chromosome Location	chr18:12445407-12445408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLMO1-1	chr18:12443295-12448204	ENSG00000267199.1

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1573330	0.88[EUR][1000 genomes]
rs3935	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479860	0.92[JPT][hapmap]
rs485566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs486498	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs496485	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496491	0.86[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499013	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504147	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs504863	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs509989	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514831	0.92[JPT][hapmap]
rs526691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527596	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533792	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs550162	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs552405	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558090	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs562079	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs575093	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs481103	C18orf1	cis	parietal	SCAN
rs481103	FECH	trans	lymphoblastoid	seeQTL
rs481103	VAPA	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
4	chr18:12431000-12447600	Weak transcription	NH-A	brain
5	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
6	chr18:12431200-12447800	Weak transcription	NHEK	skin
7	chr18:12432600-12447000	Weak transcription	HMEC	breast
8	chr18:12433000-12448800	Weak transcription	HUVEC	blood vessel
9	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:12433200-12449200	Weak transcription	Gastric	stomach
11	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
12	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
13	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:12433400-12458600	Weak transcription	HepG2	liver
15	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
16	chr18:12435200-12449000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr18:12438200-12449200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr18:12439200-12448800	Weak transcription	NHLF	lung
19	chr18:12439400-12468200	Weak transcription	K562	blood
20	chr18:12441400-12446000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr18:12441600-12452200	Weak transcription	Hela-S3	cervix
22	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr18:12443000-12445800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr18:12443000-12446000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr18:12443200-12445600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr18:12443200-12457400	Strong transcription	HSMM	muscle
27	chr18:12443400-12445600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:12443400-12445600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr18:12443400-12445800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:12443600-12445800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr18:12443600-12446000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
32	chr18:12443600-12446000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr18:12443600-12446000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr18:12443600-12446200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr18:12443600-12454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr18:12443800-12445600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:12443800-12445600	ZNF genes & repeats	Aorta	Aorta
38	chr18:12443800-12445800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr18:12443800-12445800	Strong transcription	HSMMtube	muscle
40	chr18:12443800-12446200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr18:12444000-12445800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:12444000-12449000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr18:12444000-12460200	Weak transcription	Fetal Intestine Large	intestine
44	chr18:12444000-12467400	Weak transcription	A549	lung
45	chr18:12444200-12445600	ZNF genes & repeats	Fetal Stomach	stomach
46	chr18:12444200-12445800	ZNF genes & repeats	Liver	Liver
47	chr18:12444200-12445800	Strong transcription	Ovary	ovary
48	chr18:12444200-12463200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr18:12444400-12445800	Strong transcription	Left Ventricle	heart
50	chr18:12444400-12446000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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