Variant report

Variant	rs2758383
Chromosome Location	chr6:26682323-26682324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABT1-3	chr6:26680235-26682904	ucscGeneNc_uc003nih_2

Extended variants
information (count: 47 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1021372	0.82[EUR][1000 genomes]
rs1021373	0.82[EUR][1000 genomes]
rs1027203	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1027204	0.80[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1056667	0.81[GIH][hapmap]
rs1078679	0.81[GIH][hapmap]
rs1321482	0.83[GIH][hapmap]
rs1570061	0.83[GIH][hapmap]
rs1884947	0.82[JPT][hapmap]
rs2130657	0.85[EUR][1000 genomes]
rs2172007	0.82[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2451711	0.80[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs2451712	0.85[EUR][1000 genomes]
rs2451731	0.81[EUR][1000 genomes]
rs2451741	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2451744	0.82[EUR][1000 genomes]
rs2451750	0.84[EUR][1000 genomes]
rs2451751	0.84[EUR][1000 genomes]
rs2494692	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs2494700	0.82[EUR][1000 genomes]
rs2494701	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2494709	0.81[EUR][1000 genomes]
rs2494713	0.84[EUR][1000 genomes]
rs2494716	0.85[EUR][1000 genomes]
rs2498351	0.84[EUR][1000 genomes]
rs2498380	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2504565	0.91[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2504566	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs2504567	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2504571	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2504592	0.83[EUR][1000 genomes]
rs2504599	0.80[CHD][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap]
rs2504600	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3001369	0.83[EUR][1000 genomes]
rs3800303	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs4368798	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs6456733	0.81[GIH][hapmap]
rs6918854	0.83[GIH][hapmap]
rs6925895	0.81[GIH][hapmap]
rs7767847	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs9295701	0.82[EUR][1000 genomes]
rs9461273	0.91[GIH][hapmap]
rs9461288	0.84[EUR][1000 genomes]
rs9467798	0.82[CHB][hapmap]
rs9467810	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs9467813	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2758383	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs2758383	BTN3A3	cis	parietal	SCAN
rs2758383	BTN3A1	cis	cerebellum	SCAN
rs2758383	ZNF322B	trans	multi-tissue	Pritchard
rs2758383	ZNF204P	cis	parietal	SCAN
rs2758383	RP11-457M11.2	cis	Thyroid	GTEx
rs2758383	BTN3A2	cis	lymphoblastoid	seeQTL
rs2758383	ZNF322	cis	Artery Tibial	GTEx
rs2758383	ZNF204P	cis	cerebellum	SCAN
rs2758383	HIST1H2AL	cis	cerebellum	SCAN
rs2758383	BTN3A3	cis	cerebellum	SCAN
rs2758383	ZNF322A	cis	multi-tissue	Pritchard
rs2758383	BTN3A2	cis	cerebellum	SCAN
rs2758383	ZNF322	cis	Thyroid	GTEx
rs2758383	HMGN4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26670600-26690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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