Variant report

Variant	rs4773930
Chromosome Location	chr13:96529725-96529726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1980942	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1996054	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2389530	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2389531	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2774113	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099358	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099359	0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs3099360	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3125438	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34859372	0.85[EUR][1000 genomes]
rs473930	0.85[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.94[YRI][hapmap]
rs4773927	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs493109	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[YRI][hapmap]
rs521235	0.86[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs529306	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs539604	0.88[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap]
rs541811	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs544080	0.85[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.94[YRI][hapmap]
rs566894	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs576184	0.81[YRI][hapmap]
rs6492826	0.86[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7333045	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7992824	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7994626	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs7998903	0.89[CEU][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs816139	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816143	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9516620	0.85[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs9516626	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9525081	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9525085	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525086	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9525093	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9525095	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9525098	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561979	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9742440	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4773930	DNAJC3	cis	Esophagus Muscularis	GTEx
rs4773930	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr13:96503000-96567400	Weak transcription	NHEK	skin
8	chr13:96503200-96535200	Weak transcription	HepG2	liver
9	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
10	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
13	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
17	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
20	chr13:96503800-96548200	Weak transcription	A549	lung
21	chr13:96504000-96534000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:96506600-96554800	Weak transcription	GM12878-XiMat	blood
23	chr13:96506800-96536000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr13:96510800-96556000	Weak transcription	Psoas Muscle	Psoas
25	chr13:96511000-96537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:96511000-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:96511000-96559200	Weak transcription	Spleen	Spleen
28	chr13:96511600-96535400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr13:96514400-96536600	Weak transcription	Fetal Lung	lung
30	chr13:96515000-96553400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:96515200-96542000	Weak transcription	Gastric	stomach
32	chr13:96518200-96553200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:96519600-96546400	Weak transcription	Right Ventricle	heart
34	chr13:96520800-96559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr13:96522400-96542000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr13:96522600-96535000	Weak transcription	Hela-S3	cervix
37	chr13:96523000-96559000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr13:96523200-96547800	Weak transcription	Colon Smooth Muscle	Colon
39	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr13:96523400-96535400	Weak transcription	Osteobl	bone
41	chr13:96523800-96542200	Weak transcription	Fetal Brain Male	brain
42	chr13:96524000-96561200	Weak transcription	HMEC	breast
43	chr13:96524200-96542600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:96524200-96560400	Weak transcription	Brain Angular Gyrus	brain
45	chr13:96524400-96535600	Weak transcription	Liver	Liver
46	chr13:96524400-96537800	Weak transcription	NH-A	brain
47	chr13:96525400-96530200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:96526200-96530400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr13:96526400-96530200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr13:96526400-96531000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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