Variant report

Variant	rs16962416
Chromosome Location	chr15:49677228-49677229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10519229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1055254	1.00[CHB][hapmap]
rs11070707	1.00[CHB][hapmap]
rs1114003	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs12901416	1.00[CHB][hapmap]
rs12902107	1.00[CHB][hapmap]
rs12902794	1.00[CHB][hapmap]
rs1354919	1.00[CHB][hapmap]
rs1546424	1.00[CHB][hapmap]
rs1546425	1.00[CHB][hapmap]
rs1580996	1.00[CHB][hapmap]
rs1580997	1.00[CHB][hapmap]
rs16962166	1.00[CHB][hapmap]
rs16962169	1.00[CHB][hapmap]
rs16962171	1.00[CHB][hapmap]
rs16962174	1.00[CHB][hapmap]
rs16962175	1.00[CHB][hapmap]
rs16962177	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs16962187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16962189	1.00[CHB][hapmap]
rs16962196	1.00[CHB][hapmap]
rs16962202	1.00[CHB][hapmap]
rs16962205	1.00[CHB][hapmap]
rs16962209	1.00[CHB][hapmap]
rs16962211	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16962213	1.00[CHB][hapmap]
rs16962235	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962236	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs16962237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs16962238	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962244	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs16962256	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs16962257	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs16962259	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs16962262	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962273	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962274	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962288	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16962296	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962307	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs16962314	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs16962327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16962425	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17396612	1.00[CHB][hapmap]
rs17476940	1.00[CHB][hapmap]
rs1835227	0.83[ASN][1000 genomes]
rs1874614	1.00[CHB][hapmap]
rs2059935	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2078024	1.00[CHB][hapmap]
rs2127243	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2163097	0.83[ASN][1000 genomes]
rs2169931	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2279192	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2413958	1.00[CHB][hapmap]
rs2413963	1.00[CHB][hapmap]
rs2899437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4396481	1.00[CHB][hapmap]
rs4774539	1.00[CHB][hapmap]
rs7168633	1.00[CHB][hapmap]
rs7173759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs7178101	1.00[CHB][hapmap]
rs7179094	1.00[CHB][hapmap]
rs7179907	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs73398258	0.86[EUR][1000 genomes]
rs73398263	0.86[ASN][1000 genomes]
rs8025550	1.00[CHB][hapmap]
rs8028746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs8029506	1.00[CHB][hapmap]
rs8031680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs8040436	1.00[CHB][hapmap]
rs967892	1.00[CHB][hapmap]
rs967893	1.00[CHB][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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv442375	chr15:49652524-49684082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16962416	LNX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49673800-49683400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:49674400-49677400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr15:49676400-49683600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:49676600-49683400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:49676800-49683000	Weak transcription	H9 Cell Line	embryonic stem cell

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