Variant report

Variant	rs472788
Chromosome Location	chr13:96658855-96658856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1980942	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1996054	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2389531	0.82[EUR][1000 genomes]
rs2774113	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2849438	0.85[EUR][1000 genomes]
rs473930	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs481927	0.82[EUR][1000 genomes]
rs489179	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs493109	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs506474	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs509572	0.84[EUR][1000 genomes]
rs511029	0.83[EUR][1000 genomes]
rs517173	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs521235	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527680	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs529306	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531090	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs532399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536606	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs537571	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs539604	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs541811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544080	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs551457	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs552598	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs555221	0.82[EUR][1000 genomes]
rs561996	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs566894	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576184	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs590758	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592205	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs595696	0.84[EUR][1000 genomes]
rs6492826	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7333045	0.82[EUR][1000 genomes]
rs7992824	0.83[EUR][1000 genomes]
rs7993804	0.81[EUR][1000 genomes]
rs816139	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816143	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9516626	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525081	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525085	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9525086	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525093	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9525098	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9561979	0.85[EUR][1000 genomes]
rs9742440	0.87[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	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
3	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
4	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
5	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
6	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
7	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs472788	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96612200-96668600	Weak transcription	Pancreas	Pancrea
2	chr13:96613200-96694200	Weak transcription	A549	lung
3	chr13:96613600-96663600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr13:96616200-96668600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr13:96616800-96668400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:96617000-96663200	Weak transcription	NHDF-Ad	bronchial
7	chr13:96621600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:96622000-96668600	Weak transcription	Aorta	Aorta
9	chr13:96622200-96660400	Weak transcription	Ovary	ovary
10	chr13:96622200-96668600	Weak transcription	Fetal Kidney	kidney
11	chr13:96622200-96671400	Weak transcription	Hela-S3	cervix
12	chr13:96622200-96677200	Weak transcription	NH-A	brain
13	chr13:96622400-96668200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:96623600-96668200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:96630200-96660400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:96634800-96668200	Weak transcription	Fetal Stomach	stomach
17	chr13:96635600-96659200	Weak transcription	Adipose Nuclei	Adipose
18	chr13:96636400-96659000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:96645400-96659000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr13:96646800-96659400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr13:96647400-96659200	Weak transcription	Psoas Muscle	Psoas
22	chr13:96647600-96668200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr13:96648000-96668200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:96648200-96668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:96649800-96659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:96651000-96671800	Weak transcription	HSMM	muscle
27	chr13:96652600-96668400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:96652800-96668000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:96654600-96660000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:96655400-96668400	Weak transcription	Fetal Brain Male	brain
31	chr13:96655600-96668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:96656000-96668000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:96656000-96668000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr13:96656000-96668200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:96656000-96668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr13:96656200-96659200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr13:96656200-96660000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr13:96656400-96660000	Weak transcription	Liver	Liver
39	chr13:96657600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:96657800-96668200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr13:96657800-96677200	Weak transcription	HSMMtube	muscle
42	chr13:96658400-96668600	Weak transcription	Left Ventricle	heart
43	chr13:96658400-96668600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr13:96658600-96661400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr13:96658600-96665000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:96658800-96659200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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