Variant report

Variant	rs867410
Chromosome Location	chr1:217159448-217159449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATA17-8	chr1:217158809-217159572	l_185_chr1:217158808-217164825_testes

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11572442	1.00[YRI][hapmap]
rs11572443	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11572451	1.00[YRI][hapmap]
rs11572452	1.00[YRI][hapmap]
rs11572453	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11572454	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576344	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11587690	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12728033	0.87[JPT][hapmap]
rs12741622	0.85[CEU][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12743080	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1339213	0.86[JPT][hapmap]
rs1416538	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556891	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17041526	0.94[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs17041530	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17041540	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17044587	0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs17044788	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044802	0.87[LWK][hapmap];0.91[YRI][hapmap]
rs17044806	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044815	0.87[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap]
rs17044824	0.89[CHD][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs17044843	0.89[YRI][hapmap]
rs2818796	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs34250841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34710011	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35271799	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846797	0.85[EUR][1000 genomes]
rs4846798	0.82[CHD][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4846799	0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6690530	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643432	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643434	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71643435	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71643436	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs867408	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867409	0.85[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs920170	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs867410	NSL1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217157400-217194400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:217159200-217159800	Enhancers	HSMMtube	muscle

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