Variant report

Variant	rs3846919
Chromosome Location	chr6:56014427-56014428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1011277	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1016719	0.96[CEU][hapmap];0.92[MEX][hapmap]
rs11970688	0.81[EUR][1000 genomes]
rs12198041	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474698	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs1925152	0.81[CEU][hapmap]
rs1925165	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1925166	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs1925170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1925174	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925175	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1998699	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs1998700	0.92[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs2076473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235735	0.96[CEU][hapmap];0.96[MEX][hapmap]
rs2397203	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823468	0.96[CEU][hapmap];0.92[MEX][hapmap]
rs4452633	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4612164	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs4712120	0.81[CEU][hapmap]
rs4715576	0.85[ASN][1000 genomes]
rs4715577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4715578	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715580	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs4715583	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs4715584	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs4715594	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6920461	0.88[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6927562	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];0.84[EUR][1000 genomes]
rs6930358	0.86[ASN][1000 genomes]
rs761104	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs761105	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs764517	0.83[EUR][1000 genomes]
rs926534	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs926535	0.83[EUR][1000 genomes]
rs9296827	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs9296831	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296832	0.81[CEU][hapmap]
rs9349804	0.81[CEU][hapmap]
rs9357887	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs9357893	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs9367676	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9370479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs9370482	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs9382584	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs9396173	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs9396175	0.82[CHB][hapmap]
rs9475556	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs9475558	0.96[CEU][hapmap]
rs9475565	0.80[EUR][1000 genomes]
rs9475583	0.92[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs9475586	0.82[EUR][1000 genomes]

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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	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
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3846919	S100A4	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55920600-56018400	Weak transcription	Ovary	ovary
2	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
3	chr6:55999000-56021200	Weak transcription	Aorta	Aorta
4	chr6:56006600-56015400	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:56006600-56018600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:56010000-56016600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:56011600-56018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:56011600-56018800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:56013000-56014600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:56013000-56036400	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:56014000-56016600	Weak transcription	Fetal Lung	lung
12	chr6:56014200-56015200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links