Variant report

Variant	rs58235085
Chromosome Location	chr17:20935517-20935518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20934273..20942906-chr17:20943761..20949798,22	MCF-7	breast:
2	chr17:20916495..20920338-chr17:20933999..20937587,3	K562	blood:
3	chr17:20913654..20920338-chr17:20930133..20937587,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-7	chr17:20934173-20935705	l_1417_chr17:20919472-20934581_brain

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1045162	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1127814	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12051606	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12600703	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12601292	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12602058	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12943067	0.83[ASN][1000 genomes]
rs12946114	0.90[ASN][1000 genomes]
rs1542552	0.92[AMR][1000 genomes]
rs17770614	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054464	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2127095	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291034	0.91[ASN][1000 genomes]
rs2364326	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886105	0.86[AMR][1000 genomes]
rs4445951	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985811	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985814	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985815	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985816	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985959	0.84[ASN][1000 genomes]
rs4985963	0.89[ASN][1000 genomes]
rs4985966	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985967	0.86[ASN][1000 genomes]
rs4985968	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985969	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985971	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985975	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56323013	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59543297	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59713572	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587111	0.85[ASN][1000 genomes]
rs6587114	0.83[ASN][1000 genomes]
rs6618	0.84[ASN][1000 genomes]
rs719093	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209129	0.87[ASN][1000 genomes]
rs7216921	0.82[ASN][1000 genomes]
rs880653	0.86[AMR][1000 genomes]
rs899337	0.87[AMR][1000 genomes]
rs899340	0.85[ASN][1000 genomes]
rs9911289	0.84[ASN][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	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs58235085	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs58235085	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs58235085	RP11-344E13.3	cis	lung	GTEx
rs58235085	RP11-344E13.3	cis	Stomach	GTEx
rs58235085	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs58235085	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs58235085	RP11-344E13.3	cis	Artery Tibial	GTEx
rs58235085	RP11-344E13.3	cis	Whole Blood	GTEx
rs58235085	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs58235085	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs58235085	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs58235085	RP11-344E13.3	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:20930200-20935600	Strong transcription	GM12878-XiMat	blood
7	chr17:20931600-20937600	Enhancers	Brain Substantia Nigra	brain
8	chr17:20931800-20936600	Weak transcription	HUVEC	blood vessel
9	chr17:20931800-20937000	Genic enhancers	HSMM	muscle
10	chr17:20931800-20940200	Enhancers	Brain Cingulate Gyrus	brain
11	chr17:20932000-20935600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr17:20932000-20936400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:20932000-20936400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:20932000-20936600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr17:20932000-20937400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr17:20932000-20937400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr17:20932000-20937400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr17:20932000-20938000	Enhancers	Brain Hippocampus Middle	brain
19	chr17:20932200-20936000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:20932200-20936400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:20932200-20936400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:20932200-20937400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr17:20932200-20937800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr17:20932200-20941400	Genic enhancers	A549	lung
25	chr17:20932400-20935600	Weak transcription	Placenta	Placenta
26	chr17:20932400-20935800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
27	chr17:20932400-20935800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:20932400-20936800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr17:20932400-20937200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr17:20932400-20937400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:20932400-20937600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:20932400-20938000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr17:20932600-20935600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:20932600-20937400	Weak transcription	Colonic Mucosa	Colon
35	chr17:20932600-20937600	Enhancers	Brain Angular Gyrus	brain
36	chr17:20932600-20937800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr17:20932600-20937800	Enhancers	Adipose Nuclei	Adipose
38	chr17:20932600-20937800	Enhancers	Brain Anterior Caudate	brain
39	chr17:20932600-20940400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr17:20932800-20941800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:20933200-20936800	Weak transcription	HepG2	liver
42	chr17:20933400-20938800	Strong transcription	Hela-S3	cervix
43	chr17:20933600-20936000	Genic enhancers	Osteobl	bone
44	chr17:20933600-20937600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr17:20933800-20935800	Strong transcription	Primary B cells from cord blood	blood
46	chr17:20933800-20936800	Enhancers	Primary T cells from cord blood	blood
47	chr17:20933800-20937600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr17:20934000-20935600	Weak transcription	NHEK	skin
49	chr17:20934000-20937400	Weak transcription	Aorta	Aorta
50	chr17:20934000-20942800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links