Variant report

Variant	rs1925145
Chromosome Location	chr6:56094088-56094089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10081146	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1011277	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs1016719	0.81[CEU][hapmap]
rs11970688	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12199712	0.90[AFR][1000 genomes]
rs1319111	0.88[AFR][1000 genomes]
rs1320996	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474698	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1925143	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs1925148	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925149	0.82[AFR][1000 genomes]
rs1925152	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1925166	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1925174	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1925175	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1925189	0.81[AFR][1000 genomes]
rs1998699	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1998700	0.85[CEU][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2223598	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2223600	0.81[AFR][1000 genomes]
rs2235735	0.81[CEU][hapmap]
rs2328675	0.81[AFR][1000 genomes]
rs2397203	0.84[CEU][hapmap]
rs2397208	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs2876630	0.81[AFR][1000 genomes]
rs3823468	0.81[CEU][hapmap]
rs3846923	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs3846926	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3899394	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4140574	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4140575	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4310058	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4495274	0.81[AFR][1000 genomes]
rs4554321	0.89[AFR][1000 genomes]
rs4612164	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4712116	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712120	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4715580	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4715583	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4715584	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4715585	0.81[AFR][1000 genomes]
rs4715590	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715593	0.90[AFR][1000 genomes]
rs4715594	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4715596	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6459128	0.81[AFR][1000 genomes]
rs6459129	0.81[AFR][1000 genomes]
rs6459130	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6459133	0.81[AFR][1000 genomes]
rs6459136	0.81[AFR][1000 genomes]
rs6904899	0.90[AFR][1000 genomes]
rs6908195	0.90[AFR][1000 genomes]
rs6911907	0.81[AFR][1000 genomes]
rs6914495	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs6914892	0.88[AFR][1000 genomes]
rs6920461	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6927562	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs6933151	0.81[AFR][1000 genomes]
rs6935152	0.88[AFR][1000 genomes]
rs6936386	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6939465	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs7450147	0.90[AFR][1000 genomes]
rs761104	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs761105	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs764517	0.83[ASN][1000 genomes]
rs7741903	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7754787	0.85[AFR][1000 genomes]
rs7776118	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926534	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs926535	0.84[ASN][1000 genomes]
rs9296827	0.84[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs9296831	0.85[CEU][hapmap]
rs9296832	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296833	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349804	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357887	0.80[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9357893	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357897	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367678	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9370482	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9370486	0.81[AFR][1000 genomes]
rs9382584	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9396173	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9396175	0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9396183	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464348	0.81[AFR][1000 genomes]
rs9475556	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs9475558	0.82[CEU][hapmap]
rs9475583	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9475586	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9475593	0.81[AFR][1000 genomes]
rs9475621	0.81[AFR][1000 genomes]
rs9475641	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1925145	COL21A1	cis	Nerve Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56082200-56104800	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:56089200-56095800	Weak transcription	HMEC	breast
3	chr6:56089200-56097600	Weak transcription	Aorta	Aorta
4	chr6:56089400-56095600	Weak transcription	NHEK	skin
5	chr6:56089400-56096000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:56091000-56095800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:56092000-56097400	Weak transcription	Ovary	ovary
8	chr6:56092400-56095600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:56092600-56099800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:56092600-56100000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:56092800-56095000	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:56092800-56095600	Weak transcription	Fetal Lung	lung
13	chr6:56093000-56095600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:56093000-56095800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:56093000-56100000	Weak transcription	Osteobl	bone
16	chr6:56093200-56095800	Weak transcription	Fetal Stomach	stomach
17	chr6:56093200-56097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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