Variant report

Variant	rs13417045
Chromosome Location	chr2:183246854-183246855
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10173255	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1021090	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10497598	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10931008	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11676337	0.90[CEU][hapmap]
rs11678230	0.90[JPT][hapmap]
rs12621190	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12996836	0.80[JPT][hapmap]
rs13387603	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13392487	0.80[LWK][hapmap];0.96[YRI][hapmap]
rs13406145	0.82[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1370665	0.90[JPT][hapmap]
rs1370666	0.90[JPT][hapmap]
rs1383898	0.80[JPT][hapmap]
rs1430147	0.84[CEU][hapmap]
rs1430148	0.84[CEU][hapmap]
rs1438071	1.00[YRI][hapmap]
rs1564542	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1564543	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16823106	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16823122	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16823257	0.81[CEU][hapmap]
rs16823686	0.80[JPT][hapmap]
rs17264887	0.90[JPT][hapmap]
rs17264894	0.85[JPT][hapmap]
rs2170400	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2887199	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57452497	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58663992	0.85[EUR][1000 genomes]
rs62190186	0.87[EUR][1000 genomes]
rs62190198	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62190200	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718448	0.85[JPT][hapmap]
rs7422491	0.80[JPT][hapmap]
rs7595025	0.80[JPT][hapmap]
rs833174	0.80[JPT][hapmap]
rs833178	0.80[JPT][hapmap]
rs833181	0.80[JPT][hapmap]
rs864417	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533782	chr2:183059730-183500040	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv834481	chr2:183189758-183339577	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13417045	SSFA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183240800-183248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:183244600-183249400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:183244600-183249800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:183244800-183248400	Weak transcription	Fetal Stomach	stomach
5	chr2:183246400-183248600	Weak transcription	Aorta	Aorta
6	chr2:183246600-183248600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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