Variant report

Variant	rs12073837
Chromosome Location	chr1:221010205-221010206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10495152	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863567	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863568	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118609	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118611	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118615	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118616	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11118619	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590678	0.82[ASN][1000 genomes]
rs12057411	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12089958	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117818	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12123589	0.81[AFR][1000 genomes]
rs12124030	0.82[ASN][1000 genomes]
rs12129004	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12139139	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12145674	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335919	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1494368	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494371	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494372	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17008806	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs17596850	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17650107	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242358	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs2279638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2378425	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2642421	0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs35730037	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4143773	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61830270	0.87[ASN][1000 genomes]
rs61830289	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6541161	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668666	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673877	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693017	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7530074	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530176	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530493	0.96[ASN][1000 genomes]
rs7544735	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7553447	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs881995	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs903319	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs984676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
F-cell distribution	21326311	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12073837	BPNT1	cis	parietal	SCAN
rs12073837	C1orf115	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221002800-221016200	Weak transcription	Fetal Lung	lung
2	chr1:221003600-221012200	Weak transcription	Fetal Heart	heart
3	chr1:221004400-221014200	Weak transcription	Aorta	Aorta
4	chr1:221004800-221012800	Weak transcription	Left Ventricle	heart
5	chr1:221008000-221015800	Weak transcription	Adipose Nuclei	Adipose
6	chr1:221008200-221010600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:221008200-221015600	Weak transcription	Colon Smooth Muscle	Colon

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