Variant report

Variant	rs6803476
Chromosome Location	chr3:24533314-24533315
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24532710..24534461-chr3:24559885..24562772,2	MCF-7	breast:
2	chr3:24313227..24314767-chr3:24532940..24535103,2	MCF-7	breast:
3	chr3:24516329..24518836-chr3:24531927..24534617,2	MCF-7	breast:
4	chr3:24310060..24312090-chr3:24531891..24534333,2	MCF-7	breast:
5	chr3:24525878..24527635-chr3:24532796..24534298,2	MCF-7	breast:
6	chr3:24506686..24508341-chr3:24532233..24535009,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13090120	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865710	0.81[AMR][1000 genomes]
rs35778241	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749376	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858621	0.82[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58016799	1.00[ASN][1000 genomes]
rs6805614	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71328481	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6803476	NGLY1	cis	parietal	SCAN
rs6803476	ZNF343	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24523000-24534000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:24525600-24533800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:24526800-24534000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:24527600-24535400	Weak transcription	Lung	lung
5	chr3:24527800-24533600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:24529400-24535000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:24529800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:24529800-24534400	Weak transcription	NHDF-Ad	bronchial
9	chr3:24529800-24535200	Weak transcription	NHEK	skin
10	chr3:24530400-24534600	Enhancers	Adipose Nuclei	Adipose
11	chr3:24530800-24533600	Enhancers	HepG2	liver
12	chr3:24530800-24534400	Enhancers	Colon Smooth Muscle	Colon
13	chr3:24530800-24534800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:24531200-24533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:24531800-24533400	Enhancers	Aorta	Aorta
16	chr3:24532000-24534000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:24532000-24534000	Weak transcription	HMEC	breast
18	chr3:24532000-24534800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:24532200-24534000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:24532200-24534600	Enhancers	K562	blood
21	chr3:24532200-24535000	Weak transcription	Hela-S3	cervix
22	chr3:24532200-24535200	Weak transcription	Right Atrium	heart
23	chr3:24532200-24535400	Weak transcription	Pancreas	Pancrea
24	chr3:24532600-24533600	Weak transcription	Fetal Lung	lung
25	chr3:24532800-24533800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:24532800-24533800	Enhancers	Esophagus	oesophagus
27	chr3:24532800-24533800	Enhancers	Psoas Muscle	Psoas
28	chr3:24532800-24534200	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:24533000-24533400	Enhancers	Left Ventricle	heart
30	chr3:24533000-24533400	Enhancers	Right Ventricle	heart
31	chr3:24533000-24533600	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr3:24533000-24533600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr3:24533000-24533800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:24533000-24534000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:24533000-24534000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr3:24533000-24534200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:24533000-24534600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr3:24533200-24533400	Enhancers	H9 Cell Line	embryonic stem cell
39	chr3:24533200-24533400	Bivalent Enhancer	Brain Germinal Matrix	brain
40	chr3:24533200-24533600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:24533200-24533600	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr3:24533200-24533800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr3:24533200-24533800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:24533200-24533800	Enhancers	Gastric	stomach
45	chr3:24533200-24533800	Enhancers	Stomach Mucosa	stomach
46	chr3:24533200-24534000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
47	chr3:24533200-24534200	Flanking Active TSS	Liver	Liver
48	chr3:24533200-24534400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr3:24533200-24534600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:24533200-24534800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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