Variant report

Variant	rs9556518
Chromosome Location	chr13:96669960-96669961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1015068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114308	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11619333	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11619490	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11841021	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11842755	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11843772	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12583522	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12585387	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12860877	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411557	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1537031	0.83[AMR][1000 genomes]
rs1540609	0.83[EUR][1000 genomes]
rs17189951	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1813179	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854173	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1872161	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2026819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2129004	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2129005	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2170812	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277419	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389570	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2389571	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28649586	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34816227	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35685996	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35898412	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36079088	0.83[AMR][1000 genomes]
rs3759441	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759442	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3782989	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782990	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825424	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547218	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4771923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773933	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773934	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773935	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55822301	0.80[AMR][1000 genomes]
rs59592654	0.80[AMR][1000 genomes]
rs60677558	0.80[AMR][1000 genomes]
rs61972920	0.82[AMR][1000 genomes]
rs61973963	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492825	0.82[AMR][1000 genomes]
rs6492827	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6492828	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492829	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7317285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7320351	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7324957	0.84[AMR][1000 genomes]
rs7325690	0.82[AMR][1000 genomes]
rs7325915	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7327532	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7328164	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7328703	0.81[AMR][1000 genomes]
rs7331461	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331926	0.82[AMR][1000 genomes]
rs7332683	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7333370	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7334100	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7334508	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7335514	0.82[AMR][1000 genomes]
rs7335872	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336088	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7336373	0.83[AMR][1000 genomes]
rs7336483	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7337653	0.81[AMR][1000 genomes]
rs7338224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs764714	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7982337	0.81[AMR][1000 genomes]
rs7983589	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983843	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986005	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7990833	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991250	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7991413	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7992875	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7998353	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556509	0.80[AMR][1000 genomes]
rs9556511	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9556512	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9556513	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9556515	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9556516	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556517	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556521	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556523	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561984	0.83[AMR][1000 genomes]
rs9561985	0.82[AMR][1000 genomes]
rs9561987	0.80[AMR][1000 genomes]
rs9561988	0.83[AMR][1000 genomes]
rs9561991	0.84[AMR][1000 genomes]
rs9561995	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9561996	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9561998	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9562003	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9562005	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9562006	0.80[EUR][1000 genomes]
rs9562008	0.83[ASN][1000 genomes]
rs9562012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562014	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562015	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562017	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9562018	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562019	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562025	0.83[EUR][1000 genomes]
rs9562027	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9562032	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9634487	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9670470	0.90[AMR][1000 genomes];0.92[EUR][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	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
2	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
3	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
4	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
5	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
6	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
rs9556518	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96622200-96671400	Weak transcription	Hela-S3	cervix
3	chr13:96622200-96677200	Weak transcription	NH-A	brain
4	chr13:96651000-96671800	Weak transcription	HSMM	muscle
5	chr13:96657800-96677200	Weak transcription	HSMMtube	muscle
6	chr13:96659400-96672600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:96660200-96682200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:96660400-96678600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr13:96660600-96676600	Weak transcription	Osteobl	bone
10	chr13:96660800-96672600	Weak transcription	Liver	Liver
11	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
12	chr13:96663200-96685400	Weak transcription	HMEC	breast
13	chr13:96663800-96672600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr13:96664000-96677200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr13:96664200-96677600	Weak transcription	NHDF-Ad	bronchial
16	chr13:96664200-96684800	Weak transcription	NHLF	lung
17	chr13:96667200-96672200	Weak transcription	Brain Hippocampus Middle	brain
18	chr13:96668000-96670000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr13:96668000-96670000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr13:96668000-96670400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:96668400-96672600	Weak transcription	Brain Substantia Nigra	brain
22	chr13:96668600-96670800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr13:96668600-96671000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:96668600-96679400	Weak transcription	Fetal Brain Male	brain
25	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr13:96668800-96672800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:96668800-96673600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:96668800-96685400	Weak transcription	Gastric	stomach
29	chr13:96669000-96670400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:96669000-96683200	Weak transcription	Esophagus	oesophagus
31	chr13:96669000-96685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr13:96669000-96686200	Weak transcription	NHEK	skin
33	chr13:96669200-96670000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:96669200-96671000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:96669200-96671600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:96669200-96672400	Strong transcription	Fetal Stomach	stomach
37	chr13:96669200-96686800	Weak transcription	Right Ventricle	heart
38	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:96669400-96670800	Weak transcription	Fetal Intestine Large	intestine
40	chr13:96669400-96672000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:96669400-96672200	Weak transcription	GM12878-XiMat	blood
42	chr13:96669400-96672600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:96669400-96672600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:96669400-96673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:96669400-96676600	Weak transcription	Aorta	Aorta
46	chr13:96669400-96677000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr13:96669400-96677000	Weak transcription	Brain Germinal Matrix	brain
48	chr13:96669400-96677200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:96669400-96677200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr13:96669400-96680000	Weak transcription	Primary monocytes fromperipheralblood	blood

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