Variant report

Variant	rs34429083
Chromosome Location	chr2:54743023-54743024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11555856	0.81[EUR][1000 genomes]
rs11883910	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11904679	0.86[EUR][1000 genomes]
rs12987967	0.82[EUR][1000 genomes]
rs13006815	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007109	0.81[EUR][1000 genomes]
rs13021615	0.91[EUR][1000 genomes]
rs13036147	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391803	0.81[EUR][1000 genomes]
rs17039558	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045939	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343815	0.82[EUR][1000 genomes]
rs17415725	0.81[EUR][1000 genomes]
rs34077590	0.84[EUR][1000 genomes]
rs34094680	0.86[EUR][1000 genomes]
rs34263579	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34308676	0.91[EUR][1000 genomes]
rs34978408	0.86[EUR][1000 genomes]
rs35028480	0.80[EUR][1000 genomes]
rs36018286	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796022	0.89[EUR][1000 genomes]
rs4261758	0.90[EUR][1000 genomes]
rs4319969	0.87[EUR][1000 genomes]
rs45487791	0.84[EUR][1000 genomes]
rs57281248	0.84[EUR][1000 genomes]
rs61126015	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66693131	0.89[EUR][1000 genomes]
rs6734445	0.81[EUR][1000 genomes]
rs6734536	0.86[EUR][1000 genomes]
rs7586066	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
rs34429083	EML6	cis	Thyroid	GTEx

Chromatin state (count:74 , 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	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
5	chr2:54733600-54747000	Weak transcription	Gastric	stomach
6	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
7	chr2:54737600-54743200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
9	chr2:54738200-54743200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:54738200-54743800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:54738200-54746400	Weak transcription	NHLF	lung
13	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
14	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:54738400-54743200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:54738400-54743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:54738400-54746200	Weak transcription	A549	lung
18	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:54739400-54746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:54740200-54743800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:54740400-54743800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:54740400-54743800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:54740400-54743800	Weak transcription	Spleen	Spleen
24	chr2:54740400-54744200	Weak transcription	Lung	lung
25	chr2:54740400-54746200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:54740400-54746200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:54740400-54746200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:54740400-54746200	Weak transcription	Right Atrium	heart
29	chr2:54740400-54746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:54740400-54746400	Weak transcription	Psoas Muscle	Psoas
31	chr2:54740400-54747000	Weak transcription	Pancreas	Pancrea
32	chr2:54740400-54747800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:54740400-54751600	Weak transcription	Placenta	Placenta
34	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
35	chr2:54740600-54743200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:54740600-54743200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:54740600-54743600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:54740600-54745200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:54740600-54746200	Weak transcription	NHDF-Ad	bronchial
40	chr2:54740600-54746800	Weak transcription	Osteobl	bone
41	chr2:54740600-54747000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:54740600-54749800	Weak transcription	HepG2	liver
43	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:54740800-54745000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:54740800-54745000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:54740800-54745800	Weak transcription	Brain Angular Gyrus	brain
48	chr2:54740800-54746400	Weak transcription	Brain Anterior Caudate	brain
49	chr2:54740800-54746400	Weak transcription	HSMM	muscle
50	chr2:54740800-54746800	Weak transcription	Muscle Satellite Cultured Cells	--

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