Variant report

Variant	rs2360026
Chromosome Location	chr3:54807320-54807321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10865989	0.83[EUR][1000 genomes]
rs1346407	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1559999	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2360021	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732748	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4353779	0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs4384925	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4563383	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs515920	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs517729	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs550210	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs578032	0.91[CHB][hapmap]
rs583190	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs589281	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs652424	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6809466	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636321	0.85[CEU][hapmap]
rs838022	0.91[CHB][hapmap]
rs934083	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2360026	VPRBP	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54805200-54807400	Enhancers	Colon Smooth Muscle	Colon
2	chr3:54806000-54807600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr3:54806400-54807600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:54806400-54807600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:54806400-54807600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:54806400-54807600	Enhancers	Fetal Brain Female	brain
7	chr3:54806400-54808600	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:54806600-54807400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:54806600-54807400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:54806600-54807600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:54806600-54807800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:54806600-54808200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:54806800-54807400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:54806800-54807400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:54806800-54807400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:54806800-54807600	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:54806800-54807600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:54807000-54807600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:54807200-54807400	Enhancers	Fetal Brain Male	brain

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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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