Variant report

Variant	rs7833589
Chromosome Location	chr8:48392295-48392296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10094128	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs10099236	0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs10109113	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10441557	0.86[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs10441581	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs10957370	0.88[ASW][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs11776864	0.84[AFR][1000 genomes]
rs12547497	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13279327	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs1542721	0.87[JPT][hapmap]
rs2130411	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs4436571	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4486659	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4594029	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4873101	0.93[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4873269	0.90[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap]
rs4873386	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4873446	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4873463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873478	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs4873546	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs6472452	0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap]
rs6473996	0.93[JPT][hapmap]
rs6981485	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6986054	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs6987882	0.82[ASN][1000 genomes]
rs7462209	0.80[EUR][1000 genomes]
rs7825148	0.93[ASN][1000 genomes]
rs7827571	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs7842068	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs7846620	0.93[JPT][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1034660	chr8:48265109-48411279	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7833589	KIAA0146	cis	parietal	SCAN
rs7833589	SNAI2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48374800-48407000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr8:48384400-48396000	Weak transcription	Primary T cells from cord blood	blood
3	chr8:48384600-48396800	Weak transcription	Fetal Brain Male	brain
4	chr8:48385000-48397000	Weak transcription	Colonic Mucosa	Colon
5	chr8:48388800-48392400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr8:48388800-48396400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr8:48389000-48395200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:48389000-48396800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr8:48389200-48393200	Weak transcription	Psoas Muscle	Psoas
10	chr8:48389200-48395000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:48389200-48396200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:48389200-48397000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr8:48390200-48393400	Enhancers	Primary B cells from peripheral blood	blood
14	chr8:48390200-48393400	Enhancers	A549	lung
15	chr8:48390200-48393800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr8:48390400-48392600	Enhancers	GM12878-XiMat	blood
17	chr8:48390400-48393600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr8:48390400-48393800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr8:48390800-48392400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr8:48390800-48393800	Enhancers	Duodenum Mucosa	Duodenum
21	chr8:48390800-48395000	Weak transcription	Spleen	Spleen
22	chr8:48390800-48396800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr8:48391000-48393800	Enhancers	NHDF-Ad	bronchial
24	chr8:48391000-48394400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr8:48391000-48395400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:48391000-48396200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr8:48391200-48394000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:48391200-48396600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr8:48391200-48397000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:48391200-48397000	Weak transcription	Gastric	stomach
31	chr8:48391200-48399000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr8:48391800-48392400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:48391800-48392400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr8:48391800-48392600	Enhancers	Left Ventricle	heart
35	chr8:48391800-48393000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr8:48391800-48393400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr8:48391800-48393400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:48391800-48393800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr8:48391800-48393800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr8:48391800-48396200	Enhancers	Fetal Lung	lung
41	chr8:48392000-48392400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr8:48392000-48392400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:48392000-48392400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:48392000-48392400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr8:48392000-48392400	Enhancers	Esophagus	oesophagus
46	chr8:48392000-48392400	Enhancers	Lung	lung
47	chr8:48392000-48392400	Enhancers	Right Ventricle	heart
48	chr8:48392000-48392400	Enhancers	NH-A	brain
49	chr8:48392000-48392600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr8:48392000-48392600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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