Variant report

Variant	rs919
Chromosome Location	chr18:12446689-12446690
allele	G/T
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: 62 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11664013	1.00[CHD][hapmap]
rs12954350	1.00[ASN][1000 genomes]
rs12954606	1.00[ASN][1000 genomes]
rs12955162	1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957283	1.00[ASN][1000 genomes]
rs12958301	1.00[ASN][1000 genomes]
rs12959459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12967250	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs12971000	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17524639	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525459	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525599	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17615525	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615801	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs17615991	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs1977937	0.84[EUR][1000 genomes]
rs34054541	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34215298	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	1.00[ASN][1000 genomes]
rs34371240	1.00[ASN][1000 genomes]
rs34448712	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34460164	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34469203	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34512782	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34620743	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34737110	1.00[ASN][1000 genomes]
rs34933611	1.00[ASN][1000 genomes]
rs35160505	1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35532404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	1.00[ASN][1000 genomes]
rs35826479	1.00[ASN][1000 genomes]
rs35872229	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs71351482	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351485	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351491	1.00[ASN][1000 genomes]
rs71351492	1.00[ASN][1000 genomes]
rs71351494	1.00[ASN][1000 genomes]
rs71351495	1.00[ASN][1000 genomes]
rs71351501	1.00[ASN][1000 genomes]
rs71363149	1.00[ASN][1000 genomes]

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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs919	AP001029.1	cis	Thyroid	GTEx
rs919	SLMO1	cis	Adipose Subcutaneous	GTEx
rs919	SLMO1	cis	Nerve Tibial	GTEx
rs919	RP11-861E21.1	cis	Artery Tibial	GTEx
rs919	RP11-861E21.1	cis	Esophagus Muscularis	GTEx
rs919	AP001029.1	cis	Esophagus Muscularis	GTEx
rs919	SLMO1	cis	Esophagus Mucosa	GTEx
rs919	SLMO1	cis	Thyroid	GTEx
rs919	SLMO1	cis	cerebellum	SCAN
rs919	SPIRE1	cis	multi-tissue	Pritchard
rs919	SLMO1	cis	Artery Aorta	GTEx
rs919	AP001029.1	cis	Artery Tibial	GTEx
rs919	SLMO1	cis	Esophagus Muscularis	GTEx
rs919	SLMO1	cis	Artery Tibial	GTEx
rs919	SLMO1	cis	lung	GTEx
rs919	SLMO1	cis	Stomach	GTEx
rs919	AP001029.1	cis	Artery Aorta	GTEx

Chromatin state (count:95 , 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	chr18:12441600-12452200	Weak transcription	Hela-S3	cervix
21	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr18:12443200-12457400	Strong transcription	HSMM	muscle
23	chr18:12443600-12454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:12444000-12449000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr18:12444000-12460200	Weak transcription	Fetal Intestine Large	intestine
26	chr18:12444000-12467400	Weak transcription	A549	lung
27	chr18:12444200-12463200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr18:12444400-12448200	Weak transcription	NHDF-Ad	bronchial
29	chr18:12444400-12453400	Weak transcription	Small Intestine	intestine
30	chr18:12444400-12458600	Weak transcription	Fetal Heart	heart
31	chr18:12444400-12465800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr18:12444600-12447000	Weak transcription	Brain Substantia Nigra	brain
33	chr18:12444600-12447200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr18:12444600-12447400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr18:12444600-12448000	Weak transcription	Brain Hippocampus Middle	brain
36	chr18:12444600-12448400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr18:12444600-12449000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:12444600-12449000	Weak transcription	Brain Anterior Caudate	brain
39	chr18:12444600-12449200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr18:12444600-12450200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr18:12444600-12455800	Weak transcription	Fetal Kidney	kidney
42	chr18:12444600-12457600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr18:12444600-12459400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr18:12444600-12477600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr18:12444800-12448200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr18:12444800-12449000	Weak transcription	Right Ventricle	heart
47	chr18:12444800-12450400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr18:12444800-12450800	Strong transcription	Fetal Brain Female	brain
49	chr18:12445000-12447000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr18:12445000-12448200	Weak transcription	Adipose Nuclei	Adipose

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