Variant report

Variant	rs9556520
Chromosome Location	chr13:96685700-96685701
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1015068	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070157	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1114308	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11619333	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11619490	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11841021	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11842755	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11843772	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12583522	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12585387	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12860877	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411557	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1537031	0.83[AMR][1000 genomes]
rs1540609	0.82[EUR][1000 genomes]
rs17189951	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1813179	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1854173	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872161	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2026819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2062276	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2129004	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2129005	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2170812	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2277419	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389570	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2389571	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28649586	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34816227	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35685996	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35898412	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36079088	0.83[AMR][1000 genomes]
rs3759441	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759442	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3782989	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782990	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825424	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547218	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4771923	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4773933	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773934	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773935	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492825	0.82[AMR][1000 genomes]
rs6492827	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6492828	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492829	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7317285	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7320351	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[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];0.80[EUR][1000 genomes]
rs7327532	0.85[AMR][1000 genomes]
rs7328164	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7328703	0.81[AMR][1000 genomes]
rs7331461	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7331926	0.82[AMR][1000 genomes]
rs7332683	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7333370	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7334100	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7334508	0.95[AMR][1000 genomes];0.87[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];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336088	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7336373	0.83[AMR][1000 genomes]
rs7336483	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7337653	0.81[AMR][1000 genomes]
rs7338224	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs764714	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7982337	0.81[AMR][1000 genomes]
rs7983589	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7983843	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7986005	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7990833	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7991250	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7991413	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7992875	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998353	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9556509	0.80[AMR][1000 genomes]
rs9556511	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9556512	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9556513	0.84[AMR][1000 genomes]
rs9556515	0.89[AMR][1000 genomes]
rs9556516	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9556517	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9556518	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];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556523	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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]
rs9561996	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9561998	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9562003	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9562012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562014	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562015	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9562016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562017	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9562018	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562019	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562025	0.82[EUR][1000 genomes]
rs9562027	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9562032	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9634487	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9670470	0.90[AMR][1000 genomes];0.91[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	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
7	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9556520	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:96669000-96685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr13:96669000-96686200	Weak transcription	NHEK	skin
5	chr13:96669200-96686800	Weak transcription	Right Ventricle	heart
6	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:96669400-96694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:96669400-96704600	Weak transcription	Brain Anterior Caudate	brain
9	chr13:96669600-96686400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:96669600-96686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr13:96669600-96687000	Weak transcription	Adipose Nuclei	Adipose
12	chr13:96669800-96686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:96669800-96686400	Weak transcription	Fetal Lung	lung
14	chr13:96670400-96685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:96673000-96698400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:96673200-96686000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:96673200-96686400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:96673200-96692800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:96673200-96693400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:96673400-96686000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr13:96673400-96686000	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:96673400-96686400	Weak transcription	Liver	Liver
23	chr13:96673400-96693000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr13:96673600-96686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:96673600-96686800	Weak transcription	Left Ventricle	heart
26	chr13:96674200-96685800	Weak transcription	Fetal Intestine Large	intestine
27	chr13:96677400-96686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:96677400-96686600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr13:96677400-96693800	Weak transcription	Aorta	Aorta
30	chr13:96677600-96685800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr13:96677600-96686800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr13:96677600-96686800	Weak transcription	Ovary	ovary
33	chr13:96677600-96689400	Weak transcription	Osteobl	bone
34	chr13:96677600-96704200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr13:96677800-96693000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr13:96678000-96686000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr13:96678000-96686400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr13:96678000-96692400	Weak transcription	HepG2	liver
39	chr13:96678400-96704400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:96678600-96698800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr13:96682000-96685800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr13:96682600-96691200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr13:96682800-96693000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr13:96682800-96693800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:96683400-96686200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr13:96683400-96686400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr13:96683400-96693400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr13:96683400-96704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr13:96683800-96686000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr13:96683800-96690800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links