Variant report

Variant	rs58822703
Chromosome Location	chr3:156452074-156452075
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	chr3:156443136..156445606-chr3:156450244..156452824,2	MCF-7	breast:
2	chr3:156444709..156446238-chr3:156450175..156452710,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513495	0.97[EUR][1000 genomes]
rs12636629	0.89[EUR][1000 genomes]
rs1367312	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1529581	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373227	0.92[EUR][1000 genomes]
rs41366145	0.89[EUR][1000 genomes]
rs4364127	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55686038	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748213	0.92[ASN][1000 genomes]
rs56128116	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56152727	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56245561	0.90[EUR][1000 genomes]
rs56354026	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357051	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56836190	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56960846	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57483705	0.89[EUR][1000 genomes]
rs58263861	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59689193	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60032002	1.00[ASN][1000 genomes]
rs60178381	0.82[ASN][1000 genomes]
rs73012038	0.81[EUR][1000 genomes]
rs73012046	0.81[EUR][1000 genomes]
rs73013957	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019737	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019748	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019749	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs891463	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919520	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58822703	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs58822703	LINC00886	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156445600-156459600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:156446400-156454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:156446400-156464600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:156446400-156467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:156446800-156452400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:156447800-156453000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156447800-156457400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:156447800-156457400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:156447800-156464200	Weak transcription	HSMM	muscle
10	chr3:156447800-156464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:156447800-156465000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:156447800-156467000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:156448200-156462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:156448200-156464200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:156448400-156464600	Weak transcription	NHEK	skin
16	chr3:156450200-156455600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:156450200-156455600	Weak transcription	Fetal Intestine Small	intestine
18	chr3:156450400-156459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:156450800-156458600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:156450800-156461600	Weak transcription	HepG2	liver
21	chr3:156451000-156452200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:156451000-156454200	Weak transcription	HSMMtube	muscle
23	chr3:156451000-156455400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:156452000-156452200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:156452000-156453000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:156452000-156453200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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