Variant report

Variant	rs9525091
Chromosome Location	chr13:96588562-96588563
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1596710	0.82[EUR][1000 genomes]
rs1807900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980942	0.82[EUR][1000 genomes]
rs2389530	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2774113	0.84[EUR][1000 genomes]
rs3099359	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34482628	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34859372	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4773927	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs481927	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489179	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs509572	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs511029	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555221	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs566894	0.85[EUR][1000 genomes]
rs576184	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs595696	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6492826	0.86[EUR][1000 genomes]
rs7994626	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7998903	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816139	0.83[EUR][1000 genomes]
rs9516620	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9516626	0.84[EUR][1000 genomes]
rs9516629	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9525081	0.81[EUR][1000 genomes]
rs9525085	0.82[EUR][1000 genomes]
rs9525086	0.82[EUR][1000 genomes]
rs9525093	0.86[EUR][1000 genomes]
rs9525098	0.85[EUR][1000 genomes]
rs9561979	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9742440	0.82[EUR][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	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9525091	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs9525091	UGGT2	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96559800-96588600	Weak transcription	Gastric	stomach
3	chr13:96571000-96588600	Weak transcription	Psoas Muscle	Psoas
4	chr13:96577000-96623200	Weak transcription	NHLF	lung
5	chr13:96577200-96598000	Weak transcription	HMEC	breast
6	chr13:96577800-96608800	Weak transcription	NHEK	skin
7	chr13:96580800-96588600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:96581600-96589000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:96581600-96589600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:96583800-96588600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:96584000-96599200	Weak transcription	Colonic Mucosa	Colon
12	chr13:96584200-96588600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:96584200-96588600	Weak transcription	Esophagus	oesophagus
14	chr13:96584200-96588600	Weak transcription	Pancreas	Pancrea
15	chr13:96584200-96611000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:96584600-96592000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:96584600-96592200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:96584600-96592800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:96584800-96589000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:96585000-96592600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:96585200-96592400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:96585800-96592200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:96586000-96589000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:96586000-96601200	Weak transcription	NHDF-Ad	bronchial
25	chr13:96586200-96589000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:96586200-96592400	Strong transcription	HSMM	muscle
27	chr13:96586400-96588600	Strong transcription	Placenta	Placenta
28	chr13:96586400-96588800	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr13:96586400-96588800	Strong transcription	Hela-S3	cervix
30	chr13:96586400-96589000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
31	chr13:96586400-96589000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:96586400-96589000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
33	chr13:96586400-96589000	Strong transcription	Fetal Kidney	kidney
34	chr13:96586400-96589000	Strong transcription	A549	lung
35	chr13:96586400-96589000	ZNF genes & repeats	GM12878-XiMat	blood
36	chr13:96586400-96589000	Strong transcription	HSMMtube	muscle
37	chr13:96586400-96589000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr13:96586400-96591600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr13:96586400-96592200	Strong transcription	Liver	Liver
40	chr13:96586600-96588600	Strong transcription	Ovary	ovary
41	chr13:96586600-96589000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:96586600-96589000	ZNF genes & repeats	Fetal Lung	lung
43	chr13:96586600-96589000	Strong transcription	Right Ventricle	heart
44	chr13:96586600-96589200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:96586600-96589400	Strong transcription	Osteobl	bone
46	chr13:96586600-96592200	Strong transcription	Adipose Nuclei	Adipose
47	chr13:96586600-96601400	Weak transcription	HUVEC	blood vessel
48	chr13:96586800-96589000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:96586800-96589000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:96586800-96589000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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