Variant report

Variant	rs2789558
Chromosome Location	chr1:217159379-217159380
allele	C/G
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: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1030845	0.88[CEU][hapmap]
rs1030854	0.88[CEU][hapmap]
rs10492959	0.88[CEU][hapmap];0.80[GIH][hapmap]
rs10863284	0.86[CEU][hapmap]
rs11117734	0.82[CEU][hapmap]
rs11117740	0.83[CEU][hapmap]
rs11117741	0.83[CEU][hapmap]
rs1339221	0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1832523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1890551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1890552	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1960901	0.88[CEU][hapmap]
rs2576196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2576197	0.94[CEU][hapmap]
rs2576199	0.94[CEU][hapmap]
rs2576200	0.86[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2576201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576226	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2576227	0.83[CEU][hapmap]
rs2576229	0.82[CEU][hapmap]
rs2576230	0.83[CEU][hapmap]
rs2576271	0.94[CEU][hapmap]
rs2789557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789560	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789572	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818754	0.94[CEU][hapmap]
rs2818755	0.94[CEU][hapmap]
rs2818757	0.94[CEU][hapmap]
rs2818758	0.88[CEU][hapmap];0.80[GIH][hapmap]
rs2818765	0.89[CEU][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs2818768	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2818769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818772	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818789	0.83[CEU][hapmap]
rs2818790	0.83[CEU][hapmap]
rs2818791	0.83[CEU][hapmap]
rs2818793	0.83[CEU][hapmap]
rs2818795	0.83[CEU][hapmap]
rs2818797	0.82[CEU][hapmap]
rs2818798	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2818799	0.81[CEU][hapmap];0.95[GIH][hapmap]
rs2818801	0.94[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];0.81[ASN][1000 genomes]
rs3000609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098286	0.82[CEU][hapmap]
rs3098287	0.83[CEU][hapmap]
rs3122530	0.94[CEU][hapmap]
rs893127	0.88[CEU][hapmap]

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
rs2789558	TMEM206	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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