Variant report

Variant	rs2280505
Chromosome Location	chr3:99358539-99358540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10935892	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639371	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1355765	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs1513300	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap]
rs16841579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1708169	0.85[ASN][1000 genomes]
rs1913235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2139932	0.87[ASN][1000 genomes]
rs2280504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs496664	0.87[ASN][1000 genomes]
rs56366097	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62281825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62281826	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792355	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7613565	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9758302	0.82[ASN][1000 genomes]
rs9810097	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9815950	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9821695	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824449	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs9824784	0.82[AMR][1000 genomes]
rs9837297	0.82[AMR][1000 genomes]
rs9872048	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280505	DNAJC5B	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99354400-99362000	Active TSS	Aorta	Aorta
2	chr3:99355600-99360600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:99355800-99358600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:99355800-99358800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:99355800-99359400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:99355800-99360000	Active TSS	Right Atrium	heart
7	chr3:99356000-99359000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:99356000-99359000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:99356000-99359000	Active TSS	NH-A	brain
10	chr3:99356000-99359200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:99356000-99359200	Active TSS	HSMMtube	muscle
12	chr3:99356000-99360400	Active TSS	NHDF-Ad	bronchial
13	chr3:99356000-99360600	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:99356000-99360800	Active TSS	NHLF	lung
15	chr3:99356200-99359600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:99356400-99359400	Active TSS	Osteobl	bone
17	chr3:99357000-99358800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:99357200-99359800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:99357400-99361600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:99357600-99360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:99357600-99363800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:99357800-99358600	Flanking Active TSS	HMEC	breast
23	chr3:99357800-99363400	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:99358000-99359200	Flanking Active TSS	HUVEC	blood vessel
25	chr3:99358000-99363200	Weak transcription	Brain Anterior Caudate	brain
26	chr3:99358000-99363600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:99358000-99363800	Weak transcription	Ovary	ovary
28	chr3:99358000-99364000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:99358000-99369400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:99358200-99358600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr3:99358200-99359600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:99358200-99360000	Enhancers	Adipose Nuclei	Adipose
33	chr3:99358200-99362600	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:99358200-99363600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:99358400-99358600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:99358400-99358600	Bivalent Enhancer	Rectal Smooth Muscle	rectum
37	chr3:99358400-99358800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:99358400-99359000	Active TSS	NHEK	skin
39	chr3:99358400-99359800	Transcr. at gene 5' and 3'	HSMM	muscle

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