Variant report

Variant	rs2540523
Chromosome Location	chr13:51286083-51286084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLEU7-4	chr13:51285144-51287376	NONHSAT033864

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11839057	0.92[ASN][1000 genomes]
rs1323886	0.88[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1853558	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1853559	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492345	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2540524	0.86[EUR][1000 genomes]
rs2615123	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2706228	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2706229	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2706234	0.86[ASN][1000 genomes]
rs2706235	0.88[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2706239	0.87[ASN][1000 genomes]
rs2706241	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2706242	0.88[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2706244	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2706245	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2761840	0.86[ASN][1000 genomes]
rs2761841	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761842	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761844	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761845	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761846	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761847	0.80[EUR][1000 genomes]
rs2761849	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2761850	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2761851	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2761852	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2761853	0.86[ASN][1000 genomes]
rs2761854	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761855	0.86[ASN][1000 genomes]
rs2812235	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812238	0.86[ASN][1000 genomes]
rs2812241	0.86[ASN][1000 genomes]
rs2812242	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812243	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812244	0.86[ASN][1000 genomes]
rs2812246	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812247	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812249	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2812250	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73490089	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
2	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1037350	chr13:51272518-51447354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv561643	chr13:51286083-51306330	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2540523	VPS36	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51269400-51296800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:51282400-51286600	Weak transcription	HSMMtube	muscle
3	chr13:51282600-51287200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr13:51282600-51287400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:51282600-51287400	Enhancers	Fetal Heart	heart
6	chr13:51282800-51286800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr13:51282800-51287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:51282800-51287400	Weak transcription	Primary B cells from cord blood	blood
9	chr13:51282800-51287600	Weak transcription	Thymus	Thymus
10	chr13:51283000-51286800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr13:51283000-51287000	Weak transcription	Fetal Thymus	thymus
12	chr13:51283600-51286200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr13:51284400-51287400	Enhancers	Fetal Lung	lung
14	chr13:51285000-51287000	Weak transcription	Fetal Intestine Small	intestine
15	chr13:51285000-51289400	Enhancers	Fetal Muscle Leg	muscle
16	chr13:51285000-51290000	Weak transcription	Brain Substantia Nigra	brain
17	chr13:51285200-51288000	Weak transcription	HepG2	liver
18	chr13:51285400-51288200	Enhancers	Fetal Brain Male	brain
19	chr13:51285600-51286400	Enhancers	Brain Cingulate Gyrus	brain
20	chr13:51285600-51286400	Enhancers	Fetal Stomach	stomach
21	chr13:51285600-51286600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:51285600-51287000	Enhancers	Dnd41	blood
23	chr13:51285600-51288200	Enhancers	Fetal Brain Female	brain
24	chr13:51285800-51286200	Weak transcription	Brain Hippocampus Middle	brain
25	chr13:51285800-51286200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr13:51285800-51287200	Enhancers	Ovary	ovary
27	chr13:51285800-51287600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr13:51286000-51287000	Enhancers	Brain Angular Gyrus	brain

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