Variant report

Variant	rs7428369
Chromosome Location	chr3:159074684-159074685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11707957	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs11715734	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs13074822	1.00[CHB][hapmap];0.96[JPT][hapmap];0.93[ASN][1000 genomes]
rs1375403	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375404	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375405	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375407	0.85[CEU][hapmap]
rs1448998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1449027	0.84[CHB][hapmap]
rs1562671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1562672	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs17795566	0.89[CEU][hapmap];0.84[CHB][hapmap]
rs1975601	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2084507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2595232	0.84[CHB][hapmap]
rs2595236	0.84[CHB][hapmap]
rs2595242	0.83[CHB][hapmap]
rs2595243	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2595244	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2595245	0.89[CEU][hapmap]
rs2595246	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs2595247	0.89[CEU][hapmap];0.92[CHB][hapmap]
rs2595248	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs2621284	0.83[CHB][hapmap]
rs2621290	0.86[CEU][hapmap];0.87[CHB][hapmap]
rs2621294	0.84[CHB][hapmap]
rs2621295	0.84[CHB][hapmap]
rs2621297	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2621299	0.89[CEU][hapmap];0.84[CHB][hapmap]
rs2621300	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2621306	0.83[CHB][hapmap]
rs2621310	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs2621312	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs2621313	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs2621314	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs3851358	1.00[CEU][hapmap]
rs4680500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4680504	0.96[CEU][hapmap]
rs4680505	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6441255	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782867	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6787941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6790560	1.00[CEU][hapmap]
rs6807076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73166247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733904	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634829	0.85[CEU][hapmap]
rs7646959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649056	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][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

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159073800-159076400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:159074000-159075400	Enhancers	Brain Angular Gyrus	brain
3	chr3:159074000-159075400	Enhancers	Brain Hippocampus Middle	brain
4	chr3:159074000-159075400	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:159074000-159075800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:159074000-159076400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:159074200-159075800	Enhancers	Brain Anterior Caudate	brain
8	chr3:159074200-159075800	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:159074400-159075400	Enhancers	Brain Substantia Nigra	brain
10	chr3:159074600-159075200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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