Variant report

Variant	rs3792923
Chromosome Location	chr5:80737212-80737213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr5:80737067-80737266	K562	blood:	n/a	chr5:80737168-80737183 chr5:80737170-80737180 chr5:80737164-80737186 chr5:80737170-80737181 chr5:80737168-80737182 chr5:80737169-80737182 chr5:80737169-80737182

Variant related genes	Relation type
SSBP2	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11742106	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs13159596	0.91[ASN][1000 genomes]
rs13165194	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13177962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1541830	0.91[CEU][hapmap]
rs34672841	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35663154	0.91[ASN][1000 genomes]
rs35810595	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35856763	0.82[ASN][1000 genomes]
rs35883849	0.93[ASN][1000 genomes]
rs35995231	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764986	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62366209	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62366246	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452409	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66563423	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865796	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866727	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6877102	0.86[MEX][hapmap]
rs6883488	0.91[CEU][hapmap]
rs6894847	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895015	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896009	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702374	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725131	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7725277	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737895	0.89[ASW][hapmap];0.86[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9596	0.91[CEU][hapmap]
rs9918175	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3792923	ARSB	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80697200-80739600	Weak transcription	Left Ventricle	heart
2	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:80704400-80747600	Weak transcription	Placenta	Placenta
4	chr5:80707400-80748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:80709200-80755200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:80713600-80769200	Weak transcription	Esophagus	oesophagus
7	chr5:80716200-80767800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:80716800-80768400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:80717000-80743800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:80717200-80769200	Weak transcription	Right Ventricle	heart
11	chr5:80718000-80768800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:80718400-80752600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:80718400-80754800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:80718400-80755000	Weak transcription	GM12878-XiMat	blood
15	chr5:80719000-80769200	Weak transcription	HSMMtube	muscle
16	chr5:80721600-80739800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:80722000-80754800	Weak transcription	HSMM	muscle
18	chr5:80722400-80746600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:80722400-80754800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:80722400-80755200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:80722400-80768800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:80722400-80768800	Weak transcription	Fetal Brain Female	brain
23	chr5:80722600-80748600	Weak transcription	Ovary	ovary
24	chr5:80722600-80767600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:80722600-80768000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:80722600-80768200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:80722600-80769000	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:80722600-80769000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:80722600-80769000	Weak transcription	Fetal Brain Male	brain
30	chr5:80722600-80769000	Weak transcription	Psoas Muscle	Psoas
31	chr5:80722600-80769200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:80722800-80744200	Weak transcription	Adipose Nuclei	Adipose
33	chr5:80722800-80747800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:80722800-80748400	Weak transcription	Fetal Lung	lung
35	chr5:80722800-80755200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:80724000-80748400	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:80725200-80748000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:80725400-80755200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:80726800-80737800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:80729400-80737600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:80729400-80738200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:80729400-80738600	Strong transcription	Fetal Thymus	thymus
43	chr5:80729600-80769200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:80729800-80769200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:80730600-80767800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:80731400-80740200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:80731400-80749000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr5:80731400-80768800	Weak transcription	Fetal Kidney	kidney
49	chr5:80731800-80746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:80731800-80746400	Weak transcription	Primary B cells from cord blood	blood

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