Variant report

Variant	rs6787571
Chromosome Location	chr3:178710585-178710586
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:178708964..178712566-chr3:178712795..178715192,4	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11719643	0.85[AMR][1000 genomes]
rs12494207	0.86[ASN][1000 genomes]
rs28709897	0.96[ASN][1000 genomes]
rs4607154	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4621371	0.93[ASN][1000 genomes]
rs4955795	0.89[EUR][1000 genomes]
rs4955798	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56182354	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61323110	0.86[ASN][1000 genomes]
rs61796632	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61798163	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6797712	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800994	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72622562	0.93[ASN][1000 genomes]
rs7618985	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9823404	0.88[ASN][1000 genomes]
rs9836168	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882690	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6787571	NDUFB5	cis	parietal	SCAN
rs6787571	ATP11B	cis	parietal	SCAN
rs6787571	EIF2B5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178704200-178710600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
2	chr3:178706400-178718600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:178706800-178712800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:178707000-178711200	Weak transcription	HSMMtube	muscle
5	chr3:178707000-178718800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:178707200-178710600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:178707400-178711400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:178708200-178712800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:178708400-178715000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:178708400-178715000	Weak transcription	Aorta	Aorta
11	chr3:178708400-178718600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:178708600-178726200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:178708800-178713000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:178708800-178737800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:178709000-178713200	Strong transcription	Primary T cells from cord blood	blood
16	chr3:178709200-178724400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:178709400-178711600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:178709400-178713200	Strong transcription	HSMM	muscle
19	chr3:178709400-178714800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:178709400-178721600	Weak transcription	Primary B cells from cord blood	blood
21	chr3:178709600-178724800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:178710000-178715000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:178710200-178715000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:178710400-178711000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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