Variant report

Variant	rs1375405
Chromosome Location	chr3:159073531-159073532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1122205	0.84[YRI][hapmap]
rs11707957	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11715734	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs13074822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1349165	0.85[YRI][hapmap]
rs1349166	0.85[YRI][hapmap]
rs1375403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375407	0.81[CEU][hapmap]
rs1448998	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1449012	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1449019	0.85[YRI][hapmap]
rs1449024	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1449027	0.84[CHB][hapmap]
rs1562669	0.84[YRI][hapmap]
rs1562671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1562672	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs17795566	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs1868415	0.80[YRI][hapmap]
rs1975601	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2084507	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2365820	0.84[YRI][hapmap]
rs2365821	0.84[YRI][hapmap]
rs2595232	0.84[CHB][hapmap]
rs2595236	0.84[CHB][hapmap]
rs2595242	0.83[CHB][hapmap]
rs2595243	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2595244	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2595245	0.86[CEU][hapmap]
rs2595246	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2595247	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs2595248	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs2621284	0.83[CHB][hapmap]
rs2621290	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs2621294	0.84[CHB][hapmap]
rs2621295	0.84[CHB][hapmap]
rs2621297	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs2621299	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs2621300	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs2621306	0.83[CHB][hapmap]
rs2621310	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs2621312	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs2621313	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs2621314	0.89[CEU][hapmap];0.87[CHB][hapmap]
rs3851358	0.96[CEU][hapmap]
rs4680500	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4680504	1.00[CEU][hapmap]
rs4680505	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6441254	0.83[YRI][hapmap]
rs6441255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782867	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs6787941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6790560	0.96[CEU][hapmap]
rs6807076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810169	0.85[YRI][hapmap]
rs73166247	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733904	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7428369	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]
rs7611870	0.84[YRI][hapmap]
rs7629577	0.84[YRI][hapmap]
rs7629583	0.83[YRI][hapmap]
rs7634829	0.82[CEU][hapmap]
rs7646959	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]
rs7649056	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9283611	0.84[YRI][hapmap]
rs9681445	0.84[YRI][hapmap]
rs9809459	0.83[YRI][hapmap]
rs9825664	0.83[YRI][hapmap]
rs9855118	0.84[YRI][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:5 , 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	chr3:159073000-159074200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:159073200-159073600	Enhancers	Brain Hippocampus Middle	brain
4	chr3:159073400-159073800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:159073400-159074400	Weak transcription	Brain Substantia Nigra	brain

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