Variant report

Variant	rs2083866
Chromosome Location	chr3:146263354-146263355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:146263336-146263386	NT2-D1	testis:	n/a
2	chr3:146263345-146263395	HNPCEpiC	eye:	n/a
3	chr3:146263345-146263395	HMEC	breast:	n/a
4	chr3:146263336-146263386	Hepatocyte	liver:	n/a
5	chr3:146263336-146263386	HCT-116	colon:	n/a
6	chr3:146263336-146263386	SK-N-MC	brain:	n/a
7	chr3:146263345-146263395	AoSMC	blood vessel:	n/a
8	chr3:146263345-146263395	K562	blood:	n/a
9	chr3:146263345-146263395	AG09319	gingival:	n/a
10	chr3:146263336-146263386	CMK	blood:	n/a
11	chr3:146263336-146263386	T-47D	breast:	n/a
12	chr3:146263336-146263386	AoSMC	blood vessel:	n/a
13	chr3:146263336-146263386	GM19239	blood:	n/a
14	chr3:146263336-146263386	ECC-1	luminal epithelium:	n/a
15	chr3:146263345-146263395	NHBE	bronchial:	n/a
16	chr3:146263345-146263395	ECC-1	luminal epithelium:	n/a
17	chr3:146263345-146263395	SK-N-SH	brain:	n/a
18	chr3:146263336-146263386	HCM	heart:	n/a
19	chr3:146263345-146263395	HRE	kidney:	n/a
20	chr3:146263345-146263395	GM19239	blood:	n/a
21	chr3:146263345-146263395	HCPEpiC	choroid plexus:	n/a
22	chr3:146263336-146263386	HepG2	liver:	n/a
23	chr3:146263345-146263395	PrEC	prostate:	n/a
24	chr3:146263345-146263395	Caco-2	colon:	n/a
25	chr3:146263345-146263395	HCM	heart:	n/a
26	chr3:146263336-146263386	NH-A	brain:	n/a
27	chr3:146263345-146263395	SAEC	small airway:	n/a
28	chr3:146263336-146263386	AG09319	gingival:	n/a
29	chr3:146263345-146263395	HCT-116	colon:	n/a
30	chr3:146263345-146263395	AG04449	skin:	fetal
31	chr3:146263345-146263395	HRCEpiC	kidney:	n/a
32	chr3:146263345-146263395	IMR90	lung:	fetal
33	chr3:146263345-146263395	H1-hESC	embryonic stem cell:	embryo
34	chr3:146263345-146263395	BJ	skin:	n/a
35	chr3:146263336-146263386	Jurkat	blood:	n/a
36	chr3:146263336-146263386	SKMC	muscle:	n/a
37	chr3:146263336-146263386	SK-N-SH	brain:	n/a
38	chr3:146263345-146263395	HEEpiC	esophagus:	n/a
39	chr3:146263336-146263386	MCF-7	breast:	n/a
40	chr3:146263336-146263386	BE2_C	brain:	n/a
41	chr3:146263345-146263395	AG04450	lung:	fetal
42	chr3:146263336-146263386	NB4	blood:	n/a
43	chr3:146263345-146263395	BE2_C	brain:	n/a
44	chr3:146263345-146263395	GM12891	blood:	n/a
45	chr3:146263345-146263395	HCF	heart:	n/a
46	chr3:146263345-146263395	PANC-1	pancreas:	n/a
47	chr3:146263336-146263386	H1-hESC	embryonic stem cell:	embryo
48	chr3:146263336-146263386	PFSK-1	brain:	n/a
49	chr3:146263345-146263395	NB4	blood:	n/a
50	chr3:146263336-146263386	IMR90	lung:	fetal

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
2	chr3:146234146..146236591-chr3:146261590..146264248,2	K562	blood:

No data

Variant related genes	Relation type
PLSCR1	CpG island
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13074501	0.97[ASN][1000 genomes]
rs1546420	0.97[ASN][1000 genomes]
rs1546421	0.97[ASN][1000 genomes]
rs1579786	0.95[ASN][1000 genomes]
rs1579787	0.95[ASN][1000 genomes]
rs2587021	0.87[ASN][1000 genomes]
rs2738921	0.87[ASN][1000 genomes]
rs34682680	0.90[ASN][1000 genomes]
rs35046242	0.97[ASN][1000 genomes]
rs35416584	0.97[ASN][1000 genomes]
rs7639636	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs977757	0.97[ASN][1000 genomes]
rs977759	0.97[ASN][1000 genomes]
rs9810169	0.95[ASN][1000 genomes]
rs9813199	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9832220	0.97[ASN][1000 genomes]
rs9833135	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146260800-146263400	Active TSS	HSMM	muscle
2	chr3:146261400-146263400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:146261400-146263800	Active TSS	NHLF	lung
4	chr3:146262800-146263600	Enhancers	HepG2	liver
5	chr3:146262800-146264000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:146262800-146267600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:146262800-146268600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:146263000-146263400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:146263000-146263400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr3:146263000-146263400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:146263000-146263400	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:146263000-146263400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:146263000-146263400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:146263000-146263400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:146263000-146263400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:146263000-146263400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:146263000-146263400	Flanking Active TSS	Dnd41	blood
18	chr3:146263000-146263400	Flanking Active TSS	Hela-S3	cervix
19	chr3:146263000-146263400	Flanking Active TSS	NHEK	skin
20	chr3:146263000-146263600	Enhancers	Duodenum Mucosa	Duodenum
21	chr3:146263000-146263800	Weak transcription	GM12878-XiMat	blood
22	chr3:146263000-146264000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:146263000-146264600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:146263000-146267800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:146263200-146263400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:146263200-146263400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:146263200-146263400	Enhancers	Primary B cells from cord blood	blood
28	chr3:146263200-146263400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:146263200-146263400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:146263200-146263400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:146263200-146263400	Enhancers	Fetal Lung	lung
32	chr3:146263200-146263400	Enhancers	Small Intestine	intestine
33	chr3:146263200-146263400	Enhancers	NHDF-Ad	bronchial
34	chr3:146263200-146263600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:146263200-146263600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:146263200-146263600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:146263200-146263600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:146263200-146263600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:146263200-146263800	Enhancers	K562	blood
40	chr3:146263200-146264000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:146263200-146265600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:146263200-146265600	Enhancers	HMEC	breast
43	chr3:146263200-146267000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:146263200-146267000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:146263200-146267200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:146263200-146267400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:146263200-146267400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:146263200-146267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:146263200-146267400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:146263200-146267600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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