Variant report

Variant	rs487399
Chromosome Location	chr18:13109555-13109556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1787013	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2000666	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2509751	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs475438	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs476191	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs513897	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs516572	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs544011	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs547033	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571002	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs571218	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs693301	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878484	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs487399	CEP192	cis	Adipose Subcutaneous	GTEx
rs487399	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs487399	CEP192	cis	Nerve Tibial	GTEx
rs487399	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs487399	CEP192	cis	lung	GTEx
rs487399	CEP192	cis	Thyroid	GTEx
rs487399	CEP192	cis	Esophagus Mucosa	GTEx
rs487399	CEP192	cis	Esophagus Muscularis	GTEx
rs487399	CEP192	cis	Artery Aorta	GTEx
rs487399	CEP192	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13018600-13117400	Weak transcription	Stomach Mucosa	stomach
2	chr18:13086400-13128000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr18:13089400-13122200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr18:13091200-13110800	Weak transcription	Right Atrium	heart
5	chr18:13093000-13111200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:13093400-13111200	Strong transcription	Fetal Muscle Leg	muscle
7	chr18:13095400-13109600	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr18:13097200-13118800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:13097600-13111600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:13098800-13121200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:13099000-13109600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr18:13099200-13109600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr18:13099200-13109600	Strong transcription	Primary B cells from cord blood	blood
14	chr18:13099200-13109600	Strong transcription	Placenta	Placenta
15	chr18:13099200-13109600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr18:13099200-13124800	Strong transcription	Fetal Thymus	thymus
17	chr18:13099200-13127800	Strong transcription	Dnd41	blood
18	chr18:13099200-13128200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr18:13099400-13109600	Strong transcription	Adipose Nuclei	Adipose
20	chr18:13099400-13109600	Strong transcription	Osteobl	bone
21	chr18:13099400-13109800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr18:13099400-13110000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr18:13099400-13111400	Strong transcription	Fetal Intestine Large	intestine
24	chr18:13099400-13129400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr18:13099600-13109600	Strong transcription	Liver	Liver
26	chr18:13099600-13109600	Strong transcription	GM12878-XiMat	blood
27	chr18:13099600-13109800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr18:13099800-13111000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:13099800-13111000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:13099800-13111600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:13099800-13112000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr18:13100800-13109600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr18:13100800-13109600	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr18:13101200-13109600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr18:13101800-13112400	Weak transcription	Fetal Heart	heart
36	chr18:13102400-13109600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:13102800-13111600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr18:13103000-13111000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr18:13105400-13115400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:13106200-13130000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr18:13106800-13110600	Weak transcription	Fetal Intestine Small	intestine
42	chr18:13106800-13110600	Weak transcription	Pancreas	Pancrea
43	chr18:13106800-13110600	Weak transcription	NHEK	skin
44	chr18:13106800-13113000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:13106800-13115200	Weak transcription	Gastric	stomach
46	chr18:13106800-13115400	Weak transcription	Aorta	Aorta
47	chr18:13106800-13115600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr18:13106800-13135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr18:13107000-13110600	Weak transcription	HepG2	liver
50	chr18:13107000-13112800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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