Variant report

Variant	rs4509290
Chromosome Location	chr8:96237596-96237597
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:96223779..96226497-chr8:96236467..96238844,2	K562	blood:
2	chr8:96234981..96237972-chr8:97273758..97275615,2	MCF-7	breast:
3	chr8:96204194..96207440-chr8:96236906..96239736,3	MCF-7	breast:
4	chr8:96145188..96147902-chr8:96236051..96240393,4	K562	blood:
5	chr8:96039470..96042211-chr8:96236701..96239677,2	K562	blood:
6	chr8:96222002..96228732-chr8:96228964..96237755,16	MCF-7	breast:
7	chr8:96078172..96080522-chr8:96236324..96239006,2	MCF-7	breast:
8	chr8:96163530..96165842-chr8:96237237..96239389,2	MCF-7	breast:
9	chr8:96145749..96147825-chr8:96236619..96239498,2	MCF-7	breast:
10	chr8:96236593..96238582-chr8:96243971..96246452,2	K562	blood:
11	chr8:96234462..96239842-chr8:96279058..96283088,6	K562	blood:
12	chr8:96143360..96148175-chr8:96235522..96240876,10	MCF-7	breast:
13	chr8:96236752..96238827-chr8:128748699..128750665,2	MCF-7	breast:
14	chr8:96148421..96149927-chr8:96235607..96238590,2	K562	blood:
15	chr8:96222030..96225621-chr8:96235538..96238037,4	MCF-7	breast:
16	chr8:96232323..96234888-chr8:96235835..96240054,4	MCF-7	breast:
17	chr8:96236807..96240008-chr8:96246119..96247780,3	MCF-7	breast:
18	chr8:96096993..96099961-chr8:96235932..96238973,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000253773	Chromatin interaction
ENSG00000253351	Chromatin interaction
ENSG00000156172	Chromatin interaction
ENSG00000175895	Chromatin interaction
ENSG00000156471	Chromatin interaction
ENSG00000156469	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13258855	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13259182	0.81[YRI][hapmap]
rs13340588	0.90[AFR][1000 genomes]
rs1441393	0.81[AFR][1000 genomes]
rs1441395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1441396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4308702	0.89[JPT][hapmap]
rs62522651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6996096	0.81[AFR][1000 genomes]
rs879113	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs879998	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs879999	0.81[GIH][hapmap]
rs894151	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv523655	chr8:96205920-96239113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv16466	chr8:96206151-96243934	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv6315	chr8:96216465-96261671	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv465741	chr8:96221122-96247835	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv611759	chr8:96221122-96247835	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4509290	PHKA2	trans	parietal	SCAN
rs4509290	RPL30	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96219800-96251800	Enhancers	Primary B cells from peripheral blood	blood
2	chr8:96228000-96238800	Weak transcription	Thymus	Thymus
3	chr8:96228800-96237600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr8:96231600-96237600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr8:96231600-96241600	Enhancers	Fetal Thymus	thymus
6	chr8:96231800-96237600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:96233000-96237800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:96233200-96238800	Weak transcription	Spleen	Spleen
9	chr8:96233800-96237800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:96234000-96240000	Weak transcription	Primary T cells from cord blood	blood
11	chr8:96234200-96237600	Weak transcription	Fetal Lung	lung
12	chr8:96234200-96238000	Weak transcription	GM12878-XiMat	blood
13	chr8:96234200-96239000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:96235000-96239000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:96235000-96239600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:96235000-96239600	Enhancers	Placenta	Placenta
17	chr8:96235000-96242200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr8:96235200-96237600	Enhancers	HepG2	liver
19	chr8:96235200-96238600	Enhancers	Left Ventricle	heart
20	chr8:96235200-96238800	Enhancers	Fetal Heart	heart
21	chr8:96235200-96239000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:96235200-96239000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:96235200-96239000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr8:96235200-96239600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:96235200-96249200	Enhancers	Primary B cells from cord blood	blood
26	chr8:96235400-96238200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:96235400-96238800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:96235400-96239000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:96235400-96239000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr8:96235400-96239000	Enhancers	Brain Anterior Caudate	brain
31	chr8:96235400-96239400	Enhancers	Esophagus	oesophagus
32	chr8:96235400-96239400	Enhancers	Fetal Muscle Leg	muscle
33	chr8:96235400-96240000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr8:96235600-96239000	Enhancers	Right Ventricle	heart
35	chr8:96235600-96239200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr8:96235600-96239600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr8:96235800-96239400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr8:96235800-96240000	Enhancers	Brain Hippocampus Middle	brain
39	chr8:96236200-96237600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr8:96236200-96237600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:96236200-96237600	Weak transcription	Adipose Nuclei	Adipose
42	chr8:96236200-96237600	Weak transcription	Psoas Muscle	Psoas
43	chr8:96236200-96237600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr8:96236200-96237800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:96236200-96238800	Enhancers	HMEC	breast
46	chr8:96236200-96238800	Enhancers	Osteobl	bone
47	chr8:96236200-96239000	Enhancers	NHDF-Ad	bronchial
48	chr8:96236400-96237600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr8:96236400-96237600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr8:96236400-96237600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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