Variant report

Variant	rs16887464
Chromosome Location	chr5:57141306-57141307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12519846	0.90[EUR][1000 genomes]
rs12654378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16887469	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1821211	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1835873	0.85[ASN][1000 genomes]
rs1835875	0.85[ASN][1000 genomes]
rs2408855	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34152283	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34397458	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34711481	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35483666	0.92[EUR][1000 genomes]
rs4562008	0.83[TSI][hapmap]
rs6868222	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6892809	0.90[EUR][1000 genomes]
rs7701201	0.82[ASN][1000 genomes]
rs7717208	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7721249	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7722730	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854034	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16887464	PLK2	cis	cerebellum	SCAN
rs16887464	IL6ST	cis	cerebellum	SCAN
rs16887464	GPX8	cis	parietal	SCAN
rs16887464	DHX29	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57137600-57142800	Weak transcription	Fetal Brain Male	brain
2	chr5:57138000-57143000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:57138200-57142800	Weak transcription	Fetal Lung	lung
4	chr5:57138200-57143600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:57138400-57143400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:57138800-57142600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:57138800-57151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:57139200-57143800	Weak transcription	HMEC	breast
9	chr5:57140600-57143600	Weak transcription	HSMM	muscle
10	chr5:57140600-57146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:57140800-57147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:57141000-57146000	Weak transcription	NHEK	skin
13	chr5:57141200-57142600	Weak transcription	Fetal Muscle Leg	muscle

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Input of quick search could be:

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

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