Variant report

Variant	rs1921548
Chromosome Location	chr3:54806321-54806322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510773	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488046	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12490327	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs12490953	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496821	0.89[CHB][hapmap];0.94[CHD][hapmap]
rs13068008	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13070126	0.83[CEU][hapmap]
rs13070262	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13084347	0.82[CHD][hapmap]
rs13084602	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13086256	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs13088416	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13090131	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13092066	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095178	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13100029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1344671	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520575	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs17815840	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1882320	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882322	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2099019	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3852006	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3864001	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs3868872	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3906509	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4025824	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4083342	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6808464	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6809269	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809715	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618235	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618991	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623961	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs7636321	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1921548	PRKCD	cis	cerebellum	SCAN
rs1921548	CCDC66	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54794200-54806800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:54794400-54806600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:54805200-54807400	Enhancers	Colon Smooth Muscle	Colon
4	chr3:54805400-54806400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:54805400-54806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:54805600-54806600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:54805600-54806600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:54805600-54806800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:54805600-54806800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:54806000-54806600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:54806000-54807600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:54806200-54806600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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