Variant report

Variant	rs1715080
Chromosome Location	chr4:69176150-69176151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10033058	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11726194	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11727878	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13124352	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13130430	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1406694	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17089252	0.82[ASN][1000 genomes]
rs17089267	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1715081	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1730873	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1919898	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293594	0.82[ASN][1000 genomes]
rs2293595	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2319888	0.81[ASN][1000 genomes]
rs28656921	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34419508	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4428356	0.85[ASN][1000 genomes]
rs4860929	0.81[ASN][1000 genomes]
rs56283078	0.84[ASN][1000 genomes]
rs57105149	0.83[ASN][1000 genomes]
rs57643586	0.85[ASN][1000 genomes]
rs58108365	0.85[ASN][1000 genomes]
rs62316045	0.85[ASN][1000 genomes]
rs6812178	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666993	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1715080	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69167000-69179400	Weak transcription	HepG2	liver
2	chr4:69172800-69176200	Weak transcription	HSMM	muscle
3	chr4:69173000-69176200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:69173200-69176400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:69173400-69178600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:69173600-69176200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:69173600-69176400	Weak transcription	Primary B cells from cord blood	blood
8	chr4:69173600-69176400	Weak transcription	HSMMtube	muscle
9	chr4:69173800-69176600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:69174000-69176600	Weak transcription	Left Ventricle	heart
11	chr4:69174000-69178000	Weak transcription	Osteobl	bone
12	chr4:69174000-69182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:69174000-69182000	Weak transcription	Esophagus	oesophagus
14	chr4:69174000-69182600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:69174200-69176400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:69174400-69176200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:69174400-69176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:69174400-69176600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:69174400-69177600	Weak transcription	NHLF	lung
20	chr4:69174400-69179800	Weak transcription	Fetal Intestine Small	intestine
21	chr4:69174400-69179800	Weak transcription	Fetal Stomach	stomach
22	chr4:69174400-69182000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:69174600-69176200	Weak transcription	Liver	Liver
24	chr4:69174600-69176400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:69174600-69176400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:69174800-69176400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:69174800-69176400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:69174800-69176400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:69174800-69176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:69174800-69176400	Weak transcription	Adipose Nuclei	Adipose
31	chr4:69174800-69176400	Weak transcription	Brain Anterior Caudate	brain
32	chr4:69174800-69176400	Weak transcription	Brain Germinal Matrix	brain
33	chr4:69174800-69176400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:69174800-69176400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:69174800-69176400	Weak transcription	GM12878-XiMat	blood
36	chr4:69174800-69176600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:69174800-69176600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:69174800-69177800	Weak transcription	HMEC	breast
39	chr4:69174800-69178800	Weak transcription	Lung	lung
40	chr4:69175000-69176600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:69175000-69176600	Weak transcription	Primary T cells from cord blood	blood
42	chr4:69175000-69176600	Weak transcription	Fetal Thymus	thymus
43	chr4:69175000-69176600	Weak transcription	A549	lung
44	chr4:69175000-69176600	Weak transcription	NH-A	brain
45	chr4:69175000-69177200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:69175000-69177200	Weak transcription	Placenta	Placenta
47	chr4:69175000-69177800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:69175000-69178000	Weak transcription	Fetal Kidney	kidney
49	chr4:69175000-69178000	Weak transcription	HUVEC	blood vessel
50	chr4:69175000-69178200	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links