Variant report

Variant	rs7646959
Chromosome Location	chr3:159072815-159072816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11707957	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[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];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375404	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375407	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs1448998	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]
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];0.95[YRI][hapmap]
rs1562672	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap]
rs17795566	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs1975601	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap]
rs2084507	1.00[CHB][hapmap];0.91[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];0.86[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];0.83[GIH][hapmap]
rs2595247	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs2595248	0.89[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap]
rs2595258	0.86[GIH][hapmap]
rs2621277	0.86[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];0.83[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];0.89[GIH][hapmap]
rs2621312	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs2621313	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs2621314	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap]
rs3851358	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4645169	0.80[GIH][hapmap]
rs4680500	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[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];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441255	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[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];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs6790560	1.00[CEU][hapmap]
rs6807076	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73166247	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733904	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7428369	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]
rs7634829	0.85[CEU][hapmap]
rs7649056	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs9879667	0.80[GIH][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
rs7646959	IQCJ	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159065800-159074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:159072200-159073000	Enhancers	Fetal Brain Male	brain
3	chr3:159072800-159073000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:159072800-159073400	Enhancers	Cortex derived primary cultured neurospheres	brain

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