Variant report

Variant	rs13399553
Chromosome Location	chr2:148576732-148576733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10180655	0.87[CEU][hapmap]
rs12622150	0.85[CEU][hapmap]
rs13016893	0.80[CEU][hapmap]
rs13430086	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1895694	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2113792	0.81[CEU][hapmap]
rs2194695	0.85[CEU][hapmap]
rs2303391	1.00[YRI][hapmap]
rs3768684	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs3768686	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs3768688	0.85[CEU][hapmap]
rs55816333	0.82[EUR][1000 genomes]
rs6709182	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6713811	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6731371	0.81[GIH][hapmap]
rs7566230	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7582403	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9287411	0.85[CEU][hapmap]

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	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13399553	MMADHC	cis	parietal	SCAN
rs13399553	ACVR2A	cis	cerebellum	SCAN
rs13399553	ORC4L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148576200-148576800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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