Variant report

Variant	rs35532404
Chromosome Location	chr18:12444107-12444108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12443233..12445110-chr18:12655911..12658418,2	MCF-7	breast:
2	chr18:12373675..12375792-chr18:12443379..12445132,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000215527	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12971000	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17524639	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[ASN][1000 genomes]
rs17525459	1.00[ASN][1000 genomes]
rs17525599	1.00[ASN][1000 genomes]
rs17615525	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs1977937	0.83[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];0.96[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];0.91[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];0.93[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34620743	0.84[AMR][1000 genomes];0.90[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]
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];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351485	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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]
rs919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs35532404	SLMO1	cis	Stomach	GTEx
rs35532404	SLMO1	cis	Esophagus Muscularis	GTEx
rs35532404	RP11-861E21.1	cis	Esophagus Muscularis	GTEx
rs35532404	AP001029.1	cis	Thyroid	GTEx
rs35532404	AP001029.1	cis	Artery Aorta	GTEx
rs35532404	SLMO1	cis	Thyroid	GTEx
rs35532404	SLMO1	cis	Esophagus Mucosa	GTEx
rs35532404	SLMO1	cis	Artery Aorta	GTEx
rs35532404	SLMO1	cis	Adipose Subcutaneous	GTEx
rs35532404	AP001029.1	cis	Esophagus Muscularis	GTEx
rs35532404	SLMO1	cis	Artery Tibial	GTEx
rs35532404	AP001029.1	cis	Artery Tibial	GTEx
rs35532404	SLMO1	cis	Nerve Tibial	GTEx
rs35532404	SLMO1	cis	lung	GTEx
rs35532404	RP11-861E21.1	cis	Artery Tibial	GTEx

Chromatin state (count:83 , 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	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr18:12431000-12447600	Weak transcription	NH-A	brain
6	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
7	chr18:12431200-12447800	Weak transcription	NHEK	skin
8	chr18:12432600-12447000	Weak transcription	HMEC	breast
9	chr18:12433000-12448800	Weak transcription	HUVEC	blood vessel
10	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr18:12433200-12449200	Weak transcription	Gastric	stomach
12	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
13	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
14	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr18:12433400-12458600	Weak transcription	HepG2	liver
16	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
17	chr18:12435200-12444200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr18:12435200-12449000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr18:12438200-12449200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:12439200-12448800	Weak transcription	NHLF	lung
21	chr18:12439400-12468200	Weak transcription	K562	blood
22	chr18:12441400-12446000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr18:12441600-12452200	Weak transcription	Hela-S3	cervix
24	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:12443000-12444600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:12443000-12444600	ZNF genes & repeats	Fetal Lung	lung
27	chr18:12443000-12444600	ZNF genes & repeats	Osteobl	bone
28	chr18:12443000-12445800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr18:12443000-12446000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr18:12443200-12445600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr18:12443200-12457400	Strong transcription	HSMM	muscle
32	chr18:12443400-12444200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
33	chr18:12443400-12444200	ZNF genes & repeats	Ovary	ovary
34	chr18:12443400-12444600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr18:12443400-12444600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr18:12443400-12444600	ZNF genes & repeats	Fetal Kidney	kidney
37	chr18:12443400-12444800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr18:12443400-12444800	ZNF genes & repeats	Fetal Brain Female	brain
39	chr18:12443400-12445000	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr18:12443400-12445200	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr18:12443400-12445200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
42	chr18:12443400-12445400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr18:12443400-12445600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr18:12443400-12445600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr18:12443400-12445800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr18:12443600-12444200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
47	chr18:12443600-12444400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr18:12443600-12444400	Strong transcription	Fetal Heart	heart
49	chr18:12443600-12444600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
50	chr18:12443600-12444600	ZNF genes & repeats	Fetal Brain Male	brain

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