Variant report

Variant	rs7747376
Chromosome Location	chr6:49896050-49896051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf141-5	chr6:49896000-49896173	l_3190_chr6:49863110-49896172_testes
2	lnc-C6orf141-5	chr6:49895998-49896114	NONHSAT113068

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12197158	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12200124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203532	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1324527	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs1337820	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1337821	0.88[ASN][1000 genomes]
rs1337822	0.88[ASN][1000 genomes]
rs1337823	0.83[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs1415732	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1535933	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1538193	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1953699	0.94[ASN][1000 genomes]
rs1970303	0.87[ASN][1000 genomes]
rs2039692	0.92[ASN][1000 genomes]
rs2147409	0.86[ASN][1000 genomes]
rs2147410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181910	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34235414	0.85[ASN][1000 genomes]
rs3900863	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4142072	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4236101	0.95[ASN][1000 genomes]
rs4711937	0.88[ASN][1000 genomes]
rs4711938	0.88[ASN][1000 genomes]
rs4715151	0.95[ASN][1000 genomes]
rs4715152	0.95[ASN][1000 genomes]
rs4715153	0.95[ASN][1000 genomes]
rs4715164	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715165	0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6458719	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6927196	0.92[ASN][1000 genomes]
rs7743942	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754156	0.88[ASN][1000 genomes]
rs7760672	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7766636	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7776086	0.95[ASN][1000 genomes]
rs7776352	0.95[ASN][1000 genomes]
rs9349509	0.83[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9357636	0.95[ASN][1000 genomes]
rs9357638	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357639	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9357641	0.88[ASN][1000 genomes]
rs9367379	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9367380	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369924	0.92[ASN][1000 genomes]
rs9369926	0.90[ASN][1000 genomes]
rs9369928	0.88[ASN][1000 genomes]
rs9381833	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395543	0.90[ASN][1000 genomes]
rs9395544	0.89[ASN][1000 genomes]
rs9395547	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9395548	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv462944	chr6:49869448-49948059	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv603091	chr6:49869448-49948059	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7747376	MUT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49892000-49896600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:49892200-49896200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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