Variant report

Variant	rs7134654
Chromosome Location	chr12:47448345-47448346
allele	C/T
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:19)

rs_ID	r²[population]
rs10785651	0.99[ASN][1000 genomes]
rs10881039	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881048	0.82[ASW][hapmap]
rs11183677	0.86[EUR][1000 genomes]
rs11183699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183706	0.99[ASN][1000 genomes]
rs11183710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183711	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989912	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34142537	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768770	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305847	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7956438	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958568	0.96[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7960974	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7971310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971796	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972871	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978950	0.84[EUR][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7134654	PFKM	cis	cerebellum	SCAN
rs7134654	RAPGEF3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47429400-47450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:47445000-47450400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:47447400-47450000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr12:47447400-47450400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:47447800-47448400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:47447800-47448800	Weak transcription	K562	blood

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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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