Variant report

Variant	rs2280668
Chromosome Location	chr7:39172024-39172025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YAE1D1-3	chr7:39171978-39172246	NONHSAT120198

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10234092	0.84[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs10242528	0.92[CEU][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap]
rs10252129	0.92[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs10951595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10951596	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951597	0.92[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs11767080	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11773046	0.92[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap]
rs11972468	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12701695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12701698	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs12701699	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1525793	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap]
rs1525799	0.84[GIH][hapmap]
rs1525800	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs17511572	0.89[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs2049496	0.92[CEU][hapmap]
rs2091323	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2392619	0.94[ASN][1000 genomes]
rs28459466	0.84[CHD][hapmap];0.93[YRI][hapmap]
rs4720311	0.92[CEU][hapmap];0.83[YRI][hapmap]
rs4723823	0.81[CHB][hapmap];0.89[YRI][hapmap]
rs4723827	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6462894	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6462895	0.87[CHD][hapmap];0.93[YRI][hapmap]
rs6956307	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6979829	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7788521	0.92[CEU][hapmap]
rs955591	0.92[CEU][hapmap];0.88[YRI][hapmap]
rs9639811	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]

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	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv887968	chr7:39123165-39198960	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv830968	chr7:39127531-39283543	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv428163	chr7:39127531-39283543	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280668	DPY19L2P1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39171200-39172600	Enhancers	Fetal Muscle Leg	muscle
2	chr7:39172000-39172200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:39172000-39172200	Enhancers	Lung	lung

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