Variant report

Variant	rs4773929
Chromosome Location	chr13:96527090-96527091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11070154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11616456	0.84[EUR][1000 genomes]
rs11616658	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11619333	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11839843	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11840966	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11841021	0.83[ASN][1000 genomes]
rs11842396	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12858210	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12870771	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12876018	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411557	0.87[ASN][1000 genomes]
rs1537030	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1537031	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17189895	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389532	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2389570	0.84[ASN][1000 genomes]
rs34738594	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35423192	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35836619	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36079088	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36101002	0.81[EUR][1000 genomes]
rs4547218	0.86[ASN][1000 genomes]
rs4773928	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55822301	0.82[ASN][1000 genomes]
rs57924129	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59592654	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60677558	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61972920	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492824	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492825	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492827	0.84[ASN][1000 genomes]
rs67447270	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7321296	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7322566	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7323150	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7323734	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7323780	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7324957	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7325690	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7325915	0.83[ASN][1000 genomes]
rs7327532	0.84[ASN][1000 genomes]
rs7328703	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7331926	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7333370	0.87[ASN][1000 genomes]
rs7333843	0.82[EUR][1000 genomes]
rs7335319	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7335514	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7336373	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7337653	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7338859	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7981923	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7982337	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7983546	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984584	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7986005	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8000849	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8002064	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9556502	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9556503	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556504	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556505	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556506	0.86[ASN][1000 genomes]
rs9556508	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9556509	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9556511	0.87[ASN][1000 genomes]
rs9556512	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556513	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556515	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9561963	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9561964	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9561967	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561969	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561971	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561973	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561974	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561975	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561976	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561981	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561984	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561985	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561987	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9561988	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561991	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9561995	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561996	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9561998	0.83[ASN][1000 genomes]
rs9562003	0.84[ASN][1000 genomes]
rs9562005	0.83[ASN][1000 genomes]
rs9562006	0.83[ASN][1000 genomes]
rs9562008	0.82[ASN][1000 genomes]
rs9670089	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9670470	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4773929	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:93 , 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	chr13:96498400-96549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:96502400-96535400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
6	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr13:96503000-96527200	Weak transcription	Fetal Kidney	kidney
8	chr13:96503000-96567400	Weak transcription	NHEK	skin
9	chr13:96503200-96527800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr13:96503200-96535200	Weak transcription	HepG2	liver
11	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
12	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
14	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
15	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr13:96503400-96528600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
20	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:96503600-96528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:96503600-96528600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
25	chr13:96503800-96548200	Weak transcription	A549	lung
26	chr13:96504000-96528600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr13:96504000-96534000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr13:96506600-96554800	Weak transcription	GM12878-XiMat	blood
29	chr13:96506800-96528400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:96506800-96528800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr13:96506800-96536000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr13:96507000-96528600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:96510800-96556000	Weak transcription	Psoas Muscle	Psoas
34	chr13:96511000-96537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr13:96511000-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr13:96511000-96559200	Weak transcription	Spleen	Spleen
37	chr13:96511400-96528400	Weak transcription	NHLF	lung
38	chr13:96511400-96528800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr13:96511600-96535400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr13:96514400-96536600	Weak transcription	Fetal Lung	lung
41	chr13:96515000-96553400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr13:96515200-96542000	Weak transcription	Gastric	stomach
43	chr13:96515400-96527800	Weak transcription	HUVEC	blood vessel
44	chr13:96518200-96553200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr13:96519600-96546400	Weak transcription	Right Ventricle	heart
46	chr13:96520800-96559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr13:96522400-96542000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr13:96522600-96535000	Weak transcription	Hela-S3	cervix
49	chr13:96523000-96528600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr13:96523000-96559000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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