Variant report

Variant	rs867409
Chromosome Location	chr1:217159063-217159064
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: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10492958	0.84[CHD][hapmap]
rs11572443	0.84[CEU][hapmap];0.85[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11572453	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11572454	0.85[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11576344	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs11587690	0.85[EUR][1000 genomes]
rs12723476	1.00[ASW][hapmap]
rs12728033	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12731437	1.00[ASW][hapmap]
rs12738035	0.81[AFR][1000 genomes]
rs12741457	1.00[ASW][hapmap]
rs12741622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743080	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759584	1.00[ASW][hapmap]
rs1339213	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1416538	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1556891	0.91[CHD][hapmap];0.87[JPT][hapmap]
rs17041530	0.85[CEU][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17041540	0.85[CEU][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17044587	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17044788	0.85[CEU][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17044806	0.85[CEU][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17044824	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17044977	1.00[ASW][hapmap]
rs17686743	0.81[AFR][1000 genomes]
rs17686866	1.00[ASW][hapmap];0.81[AFR][1000 genomes]
rs2818796	0.80[JPT][hapmap]
rs34056739	0.81[AFR][1000 genomes]
rs34096624	0.81[AFR][1000 genomes]
rs34250841	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34710011	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35271799	0.83[EUR][1000 genomes]
rs4846797	0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4846798	0.84[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4846799	0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs4846800	1.00[ASW][hapmap];0.81[AFR][1000 genomes]
rs4846801	0.81[AFR][1000 genomes]
rs6684076	1.00[ASW][hapmap]
rs6690530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71643432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71643434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71643435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71643436	1.00[AFR][1000 genomes]
rs867408	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs867410	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[JPT][hapmap];0.85[EUR][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
rs867409	NSL1	cis	cerebellum	SCAN

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

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

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