Variant report

Variant	rs12509142
Chromosome Location	chr4:102655378-102655379
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12501586	0.84[YRI][hapmap]
rs12506517	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12509873	0.96[ASN][1000 genomes]
rs13120845	0.95[ASN][1000 genomes]
rs34083726	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs35157729	0.90[ASN][1000 genomes]
rs4277781	0.86[ASN][1000 genomes]
rs4286516	0.94[ASN][1000 genomes]
rs4627868	0.89[ASN][1000 genomes]
rs6532957	0.96[ASN][1000 genomes]
rs6532966	0.85[ASN][1000 genomes]
rs6851800	0.85[ASN][1000 genomes]
rs6858663	0.85[ASN][1000 genomes]
rs7660525	0.93[ASN][1000 genomes]
rs7671144	0.94[ASN][1000 genomes]
rs7674411	0.88[ASN][1000 genomes]
rs7675129	0.86[ASN][1000 genomes]
rs871061	0.90[ASN][1000 genomes]
rs9307264	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997690	chr4:102397296-102758125	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv537201	chr4:102397296-102758125	Genic enhancers Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv879678	chr4:102569730-102658991	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv879679	chr4:102574367-102658991	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv999861	chr4:102576115-102930562	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879680	chr4:102614169-102696219	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv594954	chr4:102639502-102659750	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv879681	chr4:102641265-102769677	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12509142	EMCN	cis	parietal	SCAN
rs12509142	BDH2	cis	parietal	SCAN
rs12509142	CXXC4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102654600-102655800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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