Variant report

Variant	rs3777779
Chromosome Location	chr6:133563566-133563567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1022695	0.81[ASN][1000 genomes]
rs12211053	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145349	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2145351	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3734277	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs3756868	0.83[ASN][1000 genomes]
rs3777781	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777783	0.83[ASN][1000 genomes]
rs722488	0.83[ASN][1000 genomes]
rs973714	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[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	esv2758080	chr6:133444719-133627364	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2759470	chr6:133444719-133627364	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv470862	chr6:133492507-133600402	Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv886678	chr6:133550279-133631190	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv5483	chr6:133554303-133599338	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777779	VNN3	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133561400-133563600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:133561400-133564000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:133561400-133564400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:133561400-133564600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:133561400-133564800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:133561400-133565200	Active TSS	HSMMtube	muscle
7	chr6:133561400-133565400	Active TSS	Hela-S3	cervix
8	chr6:133561400-133565800	Active TSS	A549	lung
9	chr6:133561400-133566400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:133561600-133563600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:133561600-133563600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
12	chr6:133561600-133563600	Active TSS	Brain Substantia Nigra	brain
13	chr6:133561600-133563600	Active TSS	HSMM	muscle
14	chr6:133561600-133563800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr6:133561600-133563800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:133561600-133563800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:133561600-133563800	Active TSS	Left Ventricle	heart
18	chr6:133561600-133564000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr6:133561600-133564200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:133561600-133564200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:133561600-133564200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:133561600-133564200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:133561600-133564400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:133561600-133564400	Bivalent/Poised TSS	Thymus	Thymus
25	chr6:133561600-133565000	Active TSS	Right Ventricle	heart
26	chr6:133561600-133565200	Bivalent/Poised TSS	Fetal Thymus	thymus
27	chr6:133561600-133565200	Active TSS	Psoas Muscle	Psoas
28	chr6:133561600-133565200	Active TSS	Right Atrium	heart
29	chr6:133561600-133565200	Bivalent/Poised TSS	Osteobl	bone
30	chr6:133561600-133565400	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr6:133561600-133566000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:133561800-133563600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr6:133561800-133563600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
34	chr6:133561800-133563600	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr6:133561800-133564000	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr6:133561800-133564200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
37	chr6:133561800-133564200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr6:133561800-133564400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:133561800-133564400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr6:133561800-133564600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr6:133561800-133564600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:133561800-133564600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
43	chr6:133561800-133564800	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:133561800-133566000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:133562000-133563800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
46	chr6:133562000-133563800	Active TSS	Ovary	ovary
47	chr6:133562000-133564000	Active TSS	Aorta	Aorta
48	chr6:133562000-133564000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
49	chr6:133562000-133565400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:133562400-133563600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum

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