Variant report

Variant	rs34263579
Chromosome Location	chr2:54752891-54752892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54752145..54754517-chr2:54758567..54761057,2	MCF-7	breast:
2	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

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

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

rs_ID	r²[population]
rs10528	0.81[EUR][1000 genomes]
rs11555856	0.83[EUR][1000 genomes]
rs11883910	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11904679	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12987967	0.85[EUR][1000 genomes]
rs13006815	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13021615	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13036147	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13391803	0.82[EUR][1000 genomes]
rs17039558	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17045939	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2229503	0.81[EUR][1000 genomes]
rs34077590	0.85[EUR][1000 genomes]
rs34094680	0.88[EUR][1000 genomes]
rs34308676	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34429083	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34978408	0.88[EUR][1000 genomes]
rs36018286	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3796022	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4261758	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4319969	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45487791	0.88[EUR][1000 genomes]
rs57281248	0.85[EUR][1000 genomes]
rs61126015	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66693131	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67079536	0.84[EUR][1000 genomes]
rs6734445	0.84[EUR][1000 genomes]
rs6734536	0.88[EUR][1000 genomes]
rs7424459	0.80[EUR][1000 genomes]
rs7586066	0.82[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	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
5	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34263579	EML6	cis	Thyroid	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
3	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
4	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:54744400-54753400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:54744400-54753400	Weak transcription	Ovary	ovary
9	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
10	chr2:54744600-54753400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:54747200-54753200	Weak transcription	Fetal Brain Female	brain
14	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:54747400-54753600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:54747800-54753400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:54748200-54753600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
21	chr2:54750200-54753200	Enhancers	Fetal Heart	heart
22	chr2:54750400-54753400	Enhancers	Brain Anterior Caudate	brain
23	chr2:54750400-54753600	Enhancers	Right Ventricle	heart
24	chr2:54750600-54753600	Enhancers	Left Ventricle	heart
25	chr2:54750600-54757000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:54750800-54753200	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:54750800-54753200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr2:54750800-54753400	Weak transcription	Liver	Liver
29	chr2:54750800-54753600	Weak transcription	Brain Germinal Matrix	brain
30	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:54751000-54753200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:54751000-54753200	Weak transcription	HepG2	liver
34	chr2:54751000-54753600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:54751000-54756800	Weak transcription	Fetal Intestine Large	intestine
36	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:54751800-54753200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:54751800-54753800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:54751800-54754000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:54752000-54753200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:54752000-54753200	Enhancers	HSMM	muscle
44	chr2:54752000-54753400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:54752000-54753400	Weak transcription	Lung	lung
46	chr2:54752000-54753400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:54752000-54753600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:54752000-54753600	Weak transcription	Fetal Lung	lung
49	chr2:54752000-54753800	Weak transcription	Placenta	Placenta
50	chr2:54752000-54756200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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