Variant report

Variant	rs1816899
Chromosome Location	chr5:59895500-59895501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10939860	0.82[EUR][1000 genomes]
rs10939862	0.82[EUR][1000 genomes]
rs11739724	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11740327	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11745627	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11948543	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11951950	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11952735	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11956023	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11959922	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12186391	0.81[EUR][1000 genomes]
rs12514253	0.83[EUR][1000 genomes]
rs12515025	0.82[EUR][1000 genomes]
rs12522801	0.83[EUR][1000 genomes]
rs1379114	0.83[EUR][1000 genomes]
rs1379115	0.83[EUR][1000 genomes]
rs1379117	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1445852	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1562235	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1824120	0.82[EUR][1000 genomes]
rs1867702	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870014	0.82[EUR][1000 genomes]
rs2061250	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs206789	0.86[ASN][1000 genomes]
rs2409792	0.83[EUR][1000 genomes]
rs248911	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2591636	0.82[EUR][1000 genomes]
rs286148	0.85[ASN][1000 genomes]
rs286153	0.84[EUR][1000 genomes]
rs286154	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286155	0.84[EUR][1000 genomes]
rs2898287	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3857236	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3958943	0.83[ASN][1000 genomes]
rs4538567	0.84[EUR][1000 genomes]
rs4700379	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4700380	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55720622	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55768631	0.83[ASN][1000 genomes]
rs56137970	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56191602	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62372964	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62373023	0.90[ASN][1000 genomes]
rs62373024	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62373025	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449480	0.82[ASN][1000 genomes]
rs755077	0.82[EUR][1000 genomes]
rs7707698	0.82[EUR][1000 genomes]
rs7736518	0.81[EUR][1000 genomes]
rs9686489	0.81[EUR][1000 genomes]
rs9942410	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS 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	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1816899	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
6	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:59884800-59909200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:59885000-59895800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:59889000-59900800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:59889200-59900600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:59889200-59900800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:59889400-59911000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:59890200-59911000	Weak transcription	Fetal Intestine Small	intestine
16	chr5:59890400-59901600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:59890800-59897600	Strong transcription	HepG2	liver
18	chr5:59891000-59911200	Weak transcription	Fetal Intestine Large	intestine
19	chr5:59891200-59896400	Weak transcription	HUVEC	blood vessel
20	chr5:59891200-59909200	Weak transcription	HMEC	breast
21	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:59892000-59912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:59892200-59898600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:59892200-59898600	Weak transcription	K562	blood
25	chr5:59892800-59895800	Enhancers	Dnd41	blood
26	chr5:59893000-59911000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:59893400-59895600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:59893400-59896200	Weak transcription	Small Intestine	intestine
29	chr5:59893400-59897600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:59893600-59896400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:59893600-59897400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:59894000-59900400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:59894000-59906000	Weak transcription	Osteobl	bone
34	chr5:59894200-59896800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:59894200-59897200	Strong transcription	Placenta	Placenta
36	chr5:59894400-59896800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:59894400-59897600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:59894400-59898400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
40	chr5:59894600-59895600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:59894600-59896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:59894600-59897600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:59894800-59895600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr5:59894800-59895800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
46	chr5:59895000-59895800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:59895000-59897200	Weak transcription	NH-A	brain
48	chr5:59895000-59898600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:59895200-59898400	Weak transcription	GM12878-XiMat	blood
50	chr5:59895200-59898600	Weak transcription	Primary hematopoietic stem cells	blood

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