Variant report

Variant	rs11840966
Chromosome Location	chr13:96505527-96505528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11070154	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11616456	0.86[EUR][1000 genomes]
rs11616658	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11619333	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11839843	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11841021	0.80[ASN][1000 genomes]
rs11842396	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12858210	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12870771	0.81[EUR][1000 genomes]
rs12876018	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1411557	0.84[ASN][1000 genomes]
rs1537030	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1537031	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17189895	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389532	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2389570	0.81[ASN][1000 genomes]
rs34738594	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35423192	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35836619	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36079088	0.83[EUR][1000 genomes]
rs36101002	0.81[EUR][1000 genomes]
rs4547218	0.83[ASN][1000 genomes]
rs4773928	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773929	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57924129	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59592654	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60677558	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61972920	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492824	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492825	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6492827	0.81[ASN][1000 genomes]
rs67447270	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321296	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7322566	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7323150	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7323734	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7323780	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7324957	0.82[EUR][1000 genomes]
rs7325690	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7325915	0.80[ASN][1000 genomes]
rs7327532	0.81[ASN][1000 genomes]
rs7328703	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7331926	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7333370	0.84[ASN][1000 genomes]
rs7333843	0.83[EUR][1000 genomes]
rs7335319	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7335514	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7336373	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7337653	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7338859	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7981923	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7982337	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7983546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984584	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7986005	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8000849	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002064	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9556502	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9556503	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556504	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556505	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556506	0.83[ASN][1000 genomes]
rs9556508	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9556509	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9556511	0.84[ASN][1000 genomes]
rs9556512	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9556513	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9556515	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9561963	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561964	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561967	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561969	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561971	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561973	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561974	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561975	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561976	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561981	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9561984	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9561985	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9561987	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9561988	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9561991	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9561995	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9561996	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9562003	0.81[ASN][1000 genomes]
rs9562005	0.80[ASN][1000 genomes]
rs9562006	0.80[ASN][1000 genomes]
rs9670089	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11840966	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96487000-96510000	Weak transcription	HUVEC	blood vessel
3	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:96498400-96549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:96499400-96515400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:96502000-96522400	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:96502400-96535400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:96502600-96506400	Strong transcription	Fetal Intestine Large	intestine
9	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
10	chr13:96502800-96506600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:96502800-96506800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:96502800-96514800	Weak transcription	Gastric	stomach
13	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:96503000-96506000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:96503000-96506200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr13:96503000-96506600	Strong transcription	HSMM	muscle
17	chr13:96503000-96506800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:96503000-96506800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr13:96503000-96508600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:96503000-96510600	Weak transcription	NHLF	lung
21	chr13:96503000-96517400	Weak transcription	K562	blood
22	chr13:96503000-96522600	Weak transcription	Aorta	Aorta
23	chr13:96503000-96522600	Weak transcription	Pancreas	Pancrea
24	chr13:96503000-96523600	Weak transcription	Esophagus	oesophagus
25	chr13:96503000-96526800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:96503000-96527200	Weak transcription	Fetal Kidney	kidney
27	chr13:96503000-96567400	Weak transcription	NHEK	skin
28	chr13:96503200-96506200	Weak transcription	Right Ventricle	heart
29	chr13:96503200-96506800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:96503200-96508200	Weak transcription	Brain Anterior Caudate	brain
31	chr13:96503200-96510200	Weak transcription	Hela-S3	cervix
32	chr13:96503200-96510400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr13:96503200-96522600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:96503200-96522800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr13:96503200-96527800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr13:96503200-96535200	Weak transcription	HepG2	liver
37	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
38	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
41	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr13:96503400-96506200	Weak transcription	GM12878-XiMat	blood
44	chr13:96503400-96520400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:96503400-96521800	Weak transcription	HSMMtube	muscle
46	chr13:96503400-96522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr13:96503400-96528600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
50	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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