Variant report

Variant	rs13094259
Chromosome Location	chr3:142444625-142444626
allele	G/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10935467	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11915810	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11929069	0.92[GIH][hapmap];0.89[TSI][hapmap]
rs13060062	0.84[AMR][1000 genomes]
rs13081200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13081255	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13092601	0.85[EUR][1000 genomes]
rs17624218	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1916638	0.92[GIH][hapmap];0.89[TSI][hapmap]
rs34084493	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34941168	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs36085850	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62278490	0.85[EUR][1000 genomes]
rs62278492	0.85[EUR][1000 genomes]
rs62278493	0.85[EUR][1000 genomes]
rs62278494	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62278498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13094259	SPSB4	cis	parietal	SCAN
rs13094259	TRPC1	cis	parietal	SCAN
rs13094259	ATP1B3	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142442200-142444800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:142442200-142444800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:142442200-142444800	Active TSS	K562	blood
4	chr3:142442200-142445000	Active TSS	A549	lung
5	chr3:142442400-142444800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:142442400-142444800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:142442400-142444800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:142442400-142444800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:142442400-142445000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:142443800-142445200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:142444000-142452600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:142444200-142444800	Active TSS	HepG2	liver
13	chr3:142444200-142445000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:142444200-142445000	Active TSS	Fetal Brain Female	brain
15	chr3:142444200-142445200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:142444200-142467400	Weak transcription	HSMM	muscle
17	chr3:142444400-142444800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:142444400-142445000	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr3:142444400-142445000	Enhancers	Fetal Lung	lung
20	chr3:142444400-142445200	Enhancers	Brain Hippocampus Middle	brain
21	chr3:142444400-142445200	Enhancers	Fetal Heart	heart
22	chr3:142444400-142445200	Enhancers	HUVEC	blood vessel
23	chr3:142444400-142445200	Enhancers	Osteobl	bone
24	chr3:142444400-142446400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:142444400-142451000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:142444400-142451200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:142444400-142454400	Weak transcription	Ovary	ovary
28	chr3:142444400-142467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:142444400-142469600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:142444600-142444800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:142444600-142444800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:142444600-142444800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:142444600-142445000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:142444600-142445000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr3:142444600-142445000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:142444600-142445000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:142444600-142445000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:142444600-142445000	Enhancers	Brain Germinal Matrix	brain
39	chr3:142444600-142445000	Weak transcription	Fetal Brain Male	brain
40	chr3:142444600-142445200	Enhancers	Brain Angular Gyrus	brain
41	chr3:142444600-142445200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:142444600-142445200	Enhancers	HMEC	breast
43	chr3:142444600-142445200	Enhancers	NHDF-Ad	bronchial
44	chr3:142444600-142445800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:142444600-142445800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:142444600-142446000	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:142444600-142446200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:142444600-142451200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:142444600-142453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr3:142444600-142454200	Weak transcription	NHLF	lung

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