Variant report

Variant	rs4849182
Chromosome Location	chr2:113992201-113992202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:
2	chr2:113968482..113971643-chr2:113991034..113994286,5	MCF-7	breast:
3	chr2:113973621..113980487-chr2:113991287..113996231,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:113992118-113992240	ENSG00000189223
2	lnc-PSD4-1	chr2:113992118-113992240	ENSG00000189223

Variant related genes	Relation type
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1015753	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1015755	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1049137	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1077855	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12472361	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12998725	0.80[ASN][1000 genomes]
rs2166421	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289897	0.85[AMR][1000 genomes]
rs28522253	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2863242	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28679654	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35222158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35606997	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738913	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4849178	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849180	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6736334	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4849182	PAX8	cis	Adipose Subcutaneous	GTEx
rs4849182	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4849182	AC016683.6	cis	Muscle Skeletal	GTEx
rs4849182	AC016683.6	cis	Esophagus Mucosa	GTEx
rs4849182	AC016683.6	cis	Artery Tibial	GTEx
rs4849182	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4849182	PAX8	cis	Whole Blood	GTEx
rs4849182	AC016683.6	cis	Whole Blood	GTEx
rs4849182	AC016683.6	cis	Esophagus Muscularis	GTEx
rs4849182	AC016683.6	cis	lung	GTEx
rs4849182	PAX8	cis	lung	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113982600-113992600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:113987000-113997000	Weak transcription	Hela-S3	cervix
4	chr2:113987600-113992600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:113987800-113992800	Weak transcription	Fetal Kidney	kidney
6	chr2:113988400-113992600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:113988600-113992600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:113988800-113992400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:113988800-113992600	Weak transcription	Osteobl	bone
10	chr2:113989000-113992400	Weak transcription	Fetal Thymus	thymus
11	chr2:113989000-113992600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:113989600-113992600	Enhancers	Fetal Muscle Leg	muscle
13	chr2:113990200-113992600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:113990400-113992400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:113990400-113992400	Weak transcription	Adipose Nuclei	Adipose
16	chr2:113990400-113992600	Weak transcription	Lung	lung
17	chr2:113990400-113992600	Weak transcription	Stomach Mucosa	stomach
18	chr2:113990400-113992600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:113990600-113992400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:113990600-113992400	Weak transcription	Placenta	Placenta
21	chr2:113990600-113992600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:113991000-113992400	Enhancers	K562	blood
23	chr2:113991400-113992400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:113991400-113992400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:113991400-113992600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:113991400-113992600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:113991400-113993000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:113991400-113993000	Enhancers	NHDF-Ad	bronchial
29	chr2:113991400-113993000	Enhancers	NHLF	lung
30	chr2:113991400-113993200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:113991600-113992400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:113991600-113992600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:113991600-113992600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:113991800-113992400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:113991800-113992400	Enhancers	Dnd41	blood
36	chr2:113991800-113992600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:113991800-113992600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:113991800-113992600	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:113991800-113992800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:113991800-113997000	Weak transcription	Spleen	Spleen
41	chr2:113992000-113992400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:113992000-113992600	Weak transcription	Primary T cells from cord blood	blood
43	chr2:113992000-113992600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:113992000-113992600	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:113992000-113992600	Weak transcription	Fetal Intestine Large	intestine
46	chr2:113992000-113992600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:113992000-113992600	Weak transcription	HSMM	muscle
48	chr2:113992000-113992600	Weak transcription	HSMMtube	muscle
49	chr2:113992000-113994800	Weak transcription	HepG2	liver
50	chr2:113992000-113997000	Weak transcription	Esophagus	oesophagus

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