Variant report

Variant	rs529538
Chromosome Location	chr18:12428617-12428618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12428003..12430631-chr18:12490469..12492690,2	K562	blood:
2	chr18:12427173..12429276-chr18:12453042..12455618,2	K562	blood:
3	chr18:12427958..12434396-chr18:12436312..12440619,6	K562	blood:
4	chr18:12422115..12425082-chr18:12427051..12428777,2	K562	blood:

Variant related genes	Relation type
ENSG00000267199	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12185471	1.00[CHB][hapmap]
rs1573330	0.82[AMR][1000 genomes]
rs1652670	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785326	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3906620	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4483914	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs499013	0.89[ASW][hapmap]
rs500300	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs503307	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556734	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[MEX][hapmap]
rs558090	0.89[ASW][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs573390	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs62095752	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7243917	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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
10	nsv909404	chr18:12409955-12438402	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv519557	chr18:12417905-12431506	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	esv3341464	chr18:12428452-12432250	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs529538	C18orf1	cis	parietal	SCAN
rs529538	C18orf19	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12410400-12430400	Weak transcription	A549	lung
2	chr18:12418200-12430400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr18:12420200-12434800	Weak transcription	Stomach Mucosa	stomach
4	chr18:12420600-12430000	Weak transcription	Pancreas	Pancrea
5	chr18:12420600-12432400	Weak transcription	Left Ventricle	heart
6	chr18:12420600-12432600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:12420600-12433600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr18:12420600-12443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr18:12421200-12429600	Weak transcription	Gastric	stomach
11	chr18:12421200-12429600	Weak transcription	Spleen	Spleen
12	chr18:12421200-12432400	Weak transcription	Esophagus	oesophagus
13	chr18:12421200-12443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
16	chr18:12421400-12430800	Weak transcription	Adipose Nuclei	Adipose
17	chr18:12421400-12431200	Weak transcription	Right Ventricle	heart
18	chr18:12421400-12433600	Weak transcription	Placenta	Placenta
19	chr18:12421400-12434600	Weak transcription	Colon Smooth Muscle	Colon
20	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr18:12421800-12428800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr18:12421800-12430400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr18:12421800-12434400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr18:12421800-12442400	Weak transcription	GM12878-XiMat	blood
25	chr18:12422000-12431800	Weak transcription	Fetal Thymus	thymus
26	chr18:12422600-12430400	Weak transcription	K562	blood
27	chr18:12424000-12430000	Weak transcription	Thymus	Thymus
28	chr18:12426600-12428800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
29	chr18:12426600-12428800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:12426600-12428800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:12426600-12428800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr18:12426600-12429000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr18:12426600-12430000	Strong transcription	Ovary	ovary
34	chr18:12426600-12433200	Strong transcription	Brain Angular Gyrus	brain
35	chr18:12426600-12434200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr18:12426600-12434600	Strong transcription	Brain Germinal Matrix	brain
37	chr18:12426600-12434600	Strong transcription	NHLF	lung
38	chr18:12426600-12434800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:12426600-12435000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr18:12426600-12435400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr18:12426600-12438600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr18:12426800-12429200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr18:12426800-12430200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr18:12426800-12431200	Strong transcription	Osteobl	bone
45	chr18:12426800-12431800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr18:12426800-12433400	Strong transcription	HepG2	liver
47	chr18:12426800-12434400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr18:12426800-12436400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr18:12427000-12430200	Weak transcription	NHEK	skin
50	chr18:12427000-12430400	Strong transcription	Fetal Intestine Large	intestine

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