Variant report

Variant	rs583190
Chromosome Location	chr3:54727077-54727078
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11707823	0.81[AMR][1000 genomes]
rs1346407	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1559999	0.85[CEU][hapmap]
rs2360021	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs2360026	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs3732748	0.82[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs4384925	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs515920	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs517729	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs517738	0.81[ASN][1000 genomes]
rs550210	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs578032	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs589281	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs604132	0.80[CEU][hapmap]
rs652424	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6809466	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs838022	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs934083	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs583190	VPRBP	cis	cerebellum	SCAN
rs583190	ITIH4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54713600-54743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54725600-54730200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:54725600-54731200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:54725800-54728200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54725800-54728400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:54725800-54729800	Weak transcription	HMEC	breast
7	chr3:54725800-54730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:54725800-54730000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:54725800-54730200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:54725800-54730400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:54725800-54731600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:54725800-54731600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:54726000-54730200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:54726000-54731400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:54726600-54730400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:54726600-54731400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:54726800-54728400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:54726800-54731400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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