Variant report

Variant	rs1448998
Chromosome Location	chr3:159061706-159061707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11707957	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11715734	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13074822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1375403	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375404	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375407	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs1449012	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1449024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs1449027	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs1562671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs1562672	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap]
rs17795566	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs1975601	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap]
rs2084507	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs2595232	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs2595236	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs2595242	0.83[CHB][hapmap]
rs2595243	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap]
rs2595244	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2595245	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2595246	0.89[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap]
rs2595247	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs2595248	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs2595258	0.84[GIH][hapmap]
rs2621277	0.84[GIH][hapmap]
rs2621284	0.83[CHB][hapmap]
rs2621290	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs2621294	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs2621295	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs2621297	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap]
rs2621299	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2621300	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2621306	0.83[CHB][hapmap]
rs2621310	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap]
rs2621312	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap]
rs2621313	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs2621314	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap]
rs3851358	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4680500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs4680504	0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs4680505	0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441255	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782867	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6787941	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs6790560	1.00[CEU][hapmap]
rs6807076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73166247	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733904	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7428369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634829	0.85[CEU][hapmap]
rs7646959	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649056	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1448998	IQCJ	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159059400-159064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links