Variant report

Variant	rs3822591
Chromosome Location	chr5:178542241-178542242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10038484	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10057660	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10063310	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10067183	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10068311	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10072631	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10479525	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1049532	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs12659833	0.83[ASN][1000 genomes]
rs1562233	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1562234	0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2161170	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251105	0.91[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs34320394	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3776810	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3776811	0.83[ASN][1000 genomes]
rs3797590	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797615	0.88[CEU][hapmap]
rs4700780	0.83[CEU][hapmap]
rs4701032	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4701035	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4701036	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4701037	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs4701038	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701040	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4701041	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701042	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4701043	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701046	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701048	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701050	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62393088	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6601020	0.84[ASN][1000 genomes]
rs6860046	0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6864241	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6868661	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6877691	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs716782	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7718671	0.83[ASN][1000 genomes]
rs7722105	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs7722433	0.84[JPT][hapmap]
rs7727747	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7728180	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9286043	0.88[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv883222	chr5:178540975-178595870	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3822591	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL
rs3822591	ZNF879	cis	cerebellum	SCAN
rs3822591	TBC1D9B	cis	cerebellum	SCAN
rs3822591	RAB24	cis	parietal	SCAN
rs3822591	DOK3	cis	cerebellum	SCAN
rs3822591	DDX41	cis	cerebellum	SCAN
rs3822591	DKFZp686E2433	cis	Lymphoblastoid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178527800-178559800	Weak transcription	HSMM	muscle
2	chr5:178538000-178544000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:178538000-178544400	ZNF genes & repeats	Liver	Liver
4	chr5:178538000-178550000	Strong transcription	Osteobl	bone
5	chr5:178538000-178560400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:178538200-178564600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:178538400-178542800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:178538400-178544000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr5:178538600-178542800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:178538600-178543600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:178539000-178543000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:178539400-178544400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr5:178539400-178545600	ZNF genes & repeats	Fetal Stomach	stomach
14	chr5:178539600-178542400	ZNF genes & repeats	Spleen	Spleen
15	chr5:178539800-178542800	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr5:178540200-178542600	Strong transcription	HSMMtube	muscle
17	chr5:178540200-178543400	ZNF genes & repeats	Ovary	ovary
18	chr5:178540200-178543600	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr5:178540200-178543600	ZNF genes & repeats	Fetal Lung	lung
20	chr5:178540400-178544000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:178540600-178543800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr5:178541000-178547600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:178541400-178547600	Weak transcription	NHLF	lung
24	chr5:178542200-178542800	Weak transcription	Fetal Muscle Trunk	muscle

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