Variant report

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACADM-2	chr1:75987247-75987916	NONHSAT003981

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10158990	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10874314	0.85[YRI][hapmap]
rs11163435	0.82[JPT][hapmap]
rs1249780	0.82[JPT][hapmap]
rs1249781	0.82[JPT][hapmap]
rs1249785	0.82[JPT][hapmap]
rs1249795	0.82[JPT][hapmap]
rs1249811	0.82[JPT][hapmap]
rs1249814	0.82[JPT][hapmap]
rs1249815	0.82[JPT][hapmap]
rs1249816	0.82[JPT][hapmap]
rs1249822	0.82[JPT][hapmap]
rs1249849	0.82[JPT][hapmap]
rs1249850	0.82[JPT][hapmap]
rs1614816	0.82[JPT][hapmap]
rs1778456	0.82[JPT][hapmap]
rs1913124	0.82[JPT][hapmap]
rs2224101	0.81[GIH][hapmap]
rs2347218	0.82[JPT][hapmap]
rs2587031	0.82[JPT][hapmap]
rs2799050	0.82[JPT][hapmap]
rs6658825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6672579	0.82[JPT][hapmap]
rs6676591	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6691590	0.82[JPT][hapmap]
rs7518629	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs920813	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1739902	SLC44A5	cis	Esophagus Mucosa	GTEx
rs1739902	ACADM	cis	cerebellum	SCAN
rs1739902	SNORD45C	cis	parietal	SCAN
rs1739902	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs1739902	NEXN	cis	cerebellum	SCAN
rs1739902	SLC44A5	cis	Muscle Skeletal	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75983400-75987600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:75983600-75990200	Enhancers	Fetal Brain Male	brain
3	chr1:75985400-75988400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:75985800-75989000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:75986400-75987800	Enhancers	Fetal Brain Female	brain
6	chr1:75986600-75987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:75986600-75988000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:75986600-75988000	Enhancers	NH-A	brain
9	chr1:75986800-75987600	Enhancers	Ovary	ovary
10	chr1:75987200-75988200	Weak transcription	K562	blood
11	chr1:75987400-75988400	Flanking Active TSS	HUVEC	blood vessel
12	chr1:75987400-75989000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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