Variant report

Variant	rs13006815
Chromosome Location	chr2:54744814-54744815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf73-2	chr2:54743773-54744815	expReg_chr2_4103_+

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11883910	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11904679	0.82[EUR][1000 genomes]
rs13007109	0.80[EUR][1000 genomes]
rs13021615	0.87[EUR][1000 genomes]
rs13036147	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17039558	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343815	0.81[EUR][1000 genomes]
rs17415725	0.80[EUR][1000 genomes]
rs34077590	0.80[EUR][1000 genomes]
rs34094680	0.81[EUR][1000 genomes]
rs34263579	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34308676	0.87[EUR][1000 genomes]
rs34429083	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34978408	0.81[EUR][1000 genomes]
rs36018286	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796022	0.85[EUR][1000 genomes]
rs4261758	0.86[EUR][1000 genomes]
rs4319969	0.83[EUR][1000 genomes]
rs57281248	0.80[EUR][1000 genomes]
rs61126015	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66693131	0.85[EUR][1000 genomes]
rs6734536	0.81[EUR][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	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13006815	EML6	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54733600-54747000	Weak transcription	Gastric	stomach
5	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
6	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
7	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:54738200-54746400	Weak transcription	NHLF	lung
9	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
10	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:54738400-54746200	Weak transcription	A549	lung
12	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:54739400-54746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:54740400-54746200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:54740400-54746200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:54740400-54746200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:54740400-54746200	Weak transcription	Right Atrium	heart
18	chr2:54740400-54746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54740400-54746400	Weak transcription	Psoas Muscle	Psoas
20	chr2:54740400-54747000	Weak transcription	Pancreas	Pancrea
21	chr2:54740400-54747800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:54740400-54751600	Weak transcription	Placenta	Placenta
23	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
24	chr2:54740600-54745200	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:54740600-54746200	Weak transcription	NHDF-Ad	bronchial
26	chr2:54740600-54746800	Weak transcription	Osteobl	bone
27	chr2:54740600-54747000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:54740600-54749800	Weak transcription	HepG2	liver
29	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:54740800-54745000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:54740800-54745000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:54740800-54745800	Weak transcription	Brain Angular Gyrus	brain
34	chr2:54740800-54746400	Weak transcription	Brain Anterior Caudate	brain
35	chr2:54740800-54746400	Weak transcription	HSMM	muscle
36	chr2:54740800-54746800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:54740800-54747000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:54741000-54746200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:54741000-54748000	Weak transcription	Adipose Nuclei	Adipose
40	chr2:54742000-54747000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:54742400-54745200	Weak transcription	Brain Substantia Nigra	brain
42	chr2:54742400-54745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:54742400-54747400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:54742400-54748000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:54742600-54746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:54742600-54746600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:54742600-54746800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:54742600-54747800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:54742800-54750600	Weak transcription	Brain Germinal Matrix	brain
50	chr2:54743400-54748200	Enhancers	Fetal Heart	heart

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