Variant report

Variant	rs1403725
Chromosome Location	chr3:142444133-142444134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142442669..142444351-chr3:142720029..142722522,2	MCF-7	breast:
2	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
3	chr3:142443679..142445893-chr3:142461230..142463554,2	K562	blood:
4	chr3:142443663..142444164-chr3:142712657..142713473,2	K562	blood:
5	chr3:142443512..142446497-chr3:142575988..142578278,2	K562	blood:
6	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
7	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
8	chr3:142297625..142299268-chr3:142441632..142444151,3	K562	blood:
9	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
10	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1523516	0.92[EUR][1000 genomes]
rs16852615	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2883546	0.84[EUR][1000 genomes]
rs3773506	0.90[ASW][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs4541445	1.00[EUR][1000 genomes]
rs73000186	0.81[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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1403725	PLS1	cis	lymphoblastoid	seeQTL
rs1403725	TRPC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142442200-142444200	Active TSS	Aorta	Aorta
2	chr3:142442200-142444200	Active TSS	Brain Angular Gyrus	brain
3	chr3:142442200-142444200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:142442200-142444400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:142442200-142444600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:142442200-142444600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:142442200-142444600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:142442200-142444800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:142442200-142444800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:142442200-142444800	Active TSS	K562	blood
11	chr3:142442200-142445000	Active TSS	A549	lung
12	chr3:142442400-142444200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:142442400-142444200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:142442400-142444200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:142442400-142444200	Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:142442400-142444200	Active TSS	Right Ventricle	heart
17	chr3:142442400-142444200	Active TSS	HSMMtube	muscle
18	chr3:142442400-142444400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:142442400-142444400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:142442400-142444400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:142442400-142444400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr3:142442400-142444400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr3:142442400-142444400	Active TSS	Ovary	ovary
24	chr3:142442400-142444400	Active TSS	Right Atrium	heart
25	chr3:142442400-142444400	Active TSS	NHDF-Ad	bronchial
26	chr3:142442400-142444600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:142442400-142444600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:142442400-142444600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:142442400-142444600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:142442400-142444600	Active TSS	Fetal Brain Male	brain
31	chr3:142442400-142444600	Active TSS	Fetal Kidney	kidney
32	chr3:142442400-142444800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr3:142442400-142444800	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:142442400-142444800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:142442400-142444800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:142442400-142445000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr3:142442600-142444200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:142442600-142444200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:142442600-142444200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:142442600-142444200	Active TSS	Left Ventricle	heart
41	chr3:142442600-142444200	Active TSS	Placenta Amnion	Placenta Amnion
42	chr3:142442600-142444200	Active TSS	Psoas Muscle	Psoas
43	chr3:142442600-142444600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr3:142442600-142444600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:142442600-142444600	Active TSS	NHLF	lung
46	chr3:142442800-142444200	Active TSS	Small Intestine	intestine
47	chr3:142443200-142444200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:142443400-142444200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:142443400-142444200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:142443400-142444200	Flanking Active TSS	Adipose Nuclei	Adipose

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