Variant report

Variant	rs4140574
Chromosome Location	chr6:56099424-56099425
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56098481..56101054-chr6:56102369..56105137,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10081146	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1011277	0.85[CEU][hapmap]
rs1016719	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs11970688	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199712	0.82[AFR][1000 genomes]
rs12199742	0.86[YRI][hapmap]
rs1319111	0.80[AFR][1000 genomes]
rs1320996	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474698	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1925143	0.82[AFR][1000 genomes]
rs1925145	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925148	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925149	0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs1925152	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925165	0.81[CEU][hapmap]
rs1925166	0.85[CEU][hapmap]
rs1925170	0.82[CEU][hapmap]
rs1925174	0.85[CEU][hapmap]
rs1925175	0.84[CEU][hapmap]
rs1998699	0.85[CEU][hapmap]
rs1998700	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2076473	0.80[CEU][hapmap]
rs2223598	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235735	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs2397203	0.88[CEU][hapmap]
rs2397208	0.82[AFR][1000 genomes]
rs3823468	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs3846919	0.81[CEU][hapmap]
rs3846923	0.82[AFR][1000 genomes]
rs3846926	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3899394	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4140575	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4310058	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4554321	0.81[AFR][1000 genomes]
rs4612164	0.89[CEU][hapmap]
rs4712116	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4712120	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715577	0.81[CEU][hapmap]
rs4715580	0.85[CEU][hapmap]
rs4715583	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715584	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715590	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715593	0.82[AFR][1000 genomes]
rs4715594	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4715596	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459130	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6904899	0.82[AFR][1000 genomes]
rs6908195	0.82[AFR][1000 genomes]
rs6914495	0.82[AFR][1000 genomes]
rs6914892	0.80[AFR][1000 genomes]
rs6920461	0.85[JPT][hapmap]
rs6927562	0.85[CEU][hapmap]
rs6935152	0.80[AFR][1000 genomes]
rs6936386	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6939465	0.82[AFR][1000 genomes]
rs7450147	0.82[AFR][1000 genomes]
rs761104	0.85[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs761105	0.85[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs764517	0.81[EUR][1000 genomes]
rs7741903	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776118	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926534	0.85[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs926535	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296827	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9296831	0.89[CEU][hapmap]
rs9296832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349804	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357887	0.84[CEU][hapmap]
rs9357893	0.87[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9357897	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9367676	0.81[CEU][hapmap]
rs9367678	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9370479	0.81[CEU][hapmap]
rs9370482	0.85[CEU][hapmap]
rs9382584	0.85[CEU][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs9396173	0.85[CEU][hapmap]
rs9396175	0.84[JPT][hapmap]
rs9396183	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475556	0.85[CEU][hapmap]
rs9475558	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs9475583	0.89[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9475586	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9475641	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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
rs4140574	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	chr6:56092600-56099800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:56092600-56100000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:56093000-56100000	Weak transcription	Osteobl	bone
5	chr6:56096400-56099800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:56096400-56099800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:56096400-56099800	Weak transcription	A549	lung
8	chr6:56096400-56100000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:56096600-56105400	Weak transcription	Psoas Muscle	Psoas
10	chr6:56097800-56099800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:56097800-56105400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:56098000-56100000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:56098000-56106200	Weak transcription	Fetal Lung	lung
14	chr6:56099400-56100000	Enhancers	Aorta	Aorta
15	chr6:56099400-56100400	Enhancers	Fetal Stomach	stomach
16	chr6:56099400-56100400	Enhancers	Rectal Smooth Muscle	rectum
17	chr6:56099400-56101800	Enhancers	Colon Smooth Muscle	Colon

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