Variant report

Variant	rs60677558
Chromosome Location	chr13:96566430-96566431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1015068	0.80[AMR][1000 genomes]
rs11070154	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070157	0.80[AMR][1000 genomes]
rs1114308	0.80[AMR][1000 genomes]
rs11616658	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11619333	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11839843	0.80[EUR][1000 genomes]
rs11840966	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11841021	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11842396	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12858210	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12870771	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12876018	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1411557	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1537030	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1537031	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17189895	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872161	0.81[AMR][1000 genomes]
rs2026819	0.80[AMR][1000 genomes]
rs2062276	0.80[AMR][1000 genomes]
rs2389532	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389570	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28649586	0.80[AMR][1000 genomes]
rs34738594	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35423192	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35836619	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35898412	0.80[AMR][1000 genomes]
rs36079088	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36101002	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782989	0.81[AMR][1000 genomes]
rs3825424	0.81[AMR][1000 genomes]
rs4547218	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4771923	0.80[AMR][1000 genomes]
rs4773928	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4773929	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55822301	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57924129	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59592654	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61972920	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492824	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492825	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492827	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67447270	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7317285	0.80[AMR][1000 genomes]
rs7321296	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7322566	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7323150	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7323734	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7323780	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7324957	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7325690	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7325915	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7327532	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328703	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7331461	0.81[AMR][1000 genomes]
rs7331926	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7333370	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7333843	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7334100	0.81[AMR][1000 genomes]
rs7335319	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7335514	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336373	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7337653	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338224	0.80[AMR][1000 genomes]
rs7338859	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7981923	0.81[EUR][1000 genomes]
rs7982337	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7983546	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7984584	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7986005	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7998353	0.80[AMR][1000 genomes]
rs8000849	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8002064	0.81[EUR][1000 genomes]
rs9556502	0.81[EUR][1000 genomes]
rs9556503	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556504	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556505	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9556506	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9556508	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9556509	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9556511	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9556512	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9556513	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9556515	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556518	0.80[AMR][1000 genomes]
rs9556520	0.80[AMR][1000 genomes]
rs9561964	0.81[EUR][1000 genomes]
rs9561967	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561969	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561971	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561973	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561974	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561975	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561976	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561981	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561984	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561987	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561988	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561991	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9561995	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561996	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561998	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9562003	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9562005	0.88[ASN][1000 genomes]
rs9562006	0.88[ASN][1000 genomes]
rs9562007	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9562008	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9562012	0.80[AMR][1000 genomes]
rs9562015	0.80[AMR][1000 genomes]
rs9562016	0.80[AMR][1000 genomes]
rs9670470	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60677558	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:96503000-96567400	Weak transcription	NHEK	skin
4	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr13:96542400-96576800	Weak transcription	HSMMtube	muscle
8	chr13:96542400-96581600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:96543000-96581600	Weak transcription	Fetal Lung	lung
10	chr13:96543000-96581800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:96543400-96576600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:96544600-96576800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
15	chr13:96553200-96573600	Weak transcription	Osteobl	bone
16	chr13:96558400-96567200	Weak transcription	Fetal Kidney	kidney
17	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
18	chr13:96558600-96579000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr13:96559400-96568400	Weak transcription	Liver	Liver
20	chr13:96559400-96569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr13:96559600-96567800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:96559600-96576600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr13:96559600-96576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:96559600-96580800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr13:96559600-96583000	Weak transcription	Pancreas	Pancrea
26	chr13:96559600-96586400	Weak transcription	A549	lung
27	chr13:96559800-96566800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:96559800-96567800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:96559800-96567800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:96559800-96568000	Weak transcription	Aorta	Aorta
31	chr13:96559800-96580600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr13:96559800-96580600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:96559800-96583400	Weak transcription	Esophagus	oesophagus
34	chr13:96559800-96588600	Weak transcription	Gastric	stomach
35	chr13:96560000-96567400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:96560000-96567800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:96560000-96567800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr13:96560000-96567800	Weak transcription	Left Ventricle	heart
39	chr13:96560000-96567800	Weak transcription	Lung	lung
40	chr13:96560000-96567800	Weak transcription	Ovary	ovary
41	chr13:96560000-96568000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr13:96560000-96572000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr13:96560000-96581400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr13:96560000-96581600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr13:96560200-96567800	Weak transcription	Fetal Stomach	stomach
46	chr13:96560200-96581000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr13:96560400-96568000	Weak transcription	Adipose Nuclei	Adipose
48	chr13:96562600-96580600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr13:96563200-96567600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr13:96563200-96570200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links