Variant report

Variant	rs58419243
Chromosome Location	chr2:54862352-54862353
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54854025..54856092-chr2:54861803..54863797,2	K562	blood:
2	chr2:54848170..54851894-chr2:54862208..54864352,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10176359	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176445	0.96[ASN][1000 genomes]
rs10183043	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10210502	0.85[EUR][1000 genomes]
rs10528	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11555856	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892236	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896957	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11902659	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713262	0.83[EUR][1000 genomes]
rs12713263	0.83[EUR][1000 genomes]
rs12713270	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713271	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713272	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713273	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713274	0.82[ASN][1000 genomes]
rs12987967	0.85[EUR][1000 genomes]
rs13004944	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13021606	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13021615	0.83[EUR][1000 genomes]
rs13391803	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13408295	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17039558	0.85[EUR][1000 genomes]
rs17046036	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046061	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046067	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046077	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17046108	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2048370	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2229503	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271329	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34077590	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34094680	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34308676	0.85[EUR][1000 genomes]
rs34311770	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34978408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35619551	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3739109	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3796022	0.81[EUR][1000 genomes]
rs3850350	0.80[AMR][1000 genomes]
rs4261758	0.86[EUR][1000 genomes]
rs4358162	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4374410	0.81[ASN][1000 genomes]
rs4519566	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4577321	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57281248	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61126015	0.83[EUR][1000 genomes]
rs6545430	0.82[EUR][1000 genomes]
rs6545435	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66693131	0.81[EUR][1000 genomes]
rs67079536	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6721612	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724136	0.83[EUR][1000 genomes]
rs67244067	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6730876	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734445	0.84[EUR][1000 genomes]
rs6734536	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6740893	0.91[ASN][1000 genomes]
rs6741053	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72806653	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7424459	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7569127	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584223	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586066	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7602992	0.82[EUR][1000 genomes]
rs7608414	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58419243	EML6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54839000-54864200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:54839200-54866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:54839600-54862600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:54842000-54863600	Strong transcription	Fetal Brain Female	brain
8	chr2:54842400-54862800	Strong transcription	NHEK	skin
9	chr2:54842600-54892000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:54842800-54862400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:54842800-54867800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr2:54846200-54864400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:54846400-54895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:54846400-54896600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:54846600-54898000	Strong transcription	Dnd41	blood
16	chr2:54846800-54895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:54847400-54865800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:54848000-54868800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:54848600-54892400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:54850600-54864200	Genic enhancers	Liver	Liver
21	chr2:54851800-54864200	Genic enhancers	Left Ventricle	heart
22	chr2:54856600-54862600	Genic enhancers	Lung	lung
23	chr2:54857000-54862400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:54857000-54869400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:54857000-54883400	Strong transcription	Hela-S3	cervix
26	chr2:54857200-54862800	Enhancers	Right Atrium	heart
27	chr2:54857400-54862800	Strong transcription	Fetal Brain Male	brain
28	chr2:54857400-54864000	Genic enhancers	Fetal Lung	lung
29	chr2:54857800-54862400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:54858600-54863800	Strong transcription	Colonic Mucosa	Colon
31	chr2:54858600-54864200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:54858800-54864000	Genic enhancers	Fetal Thymus	thymus
33	chr2:54859400-54873400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:54859800-54864200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:54860000-54862600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:54860000-54862600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:54860000-54863000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:54860000-54863800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:54860200-54862600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:54860200-54862600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:54860200-54862800	Genic enhancers	Fetal Stomach	stomach
42	chr2:54860200-54862800	Genic enhancers	HMEC	breast
43	chr2:54860200-54863000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:54860200-54863000	Genic enhancers	Primary T cells from cord blood	blood
45	chr2:54860200-54864400	Genic enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:54860400-54862400	Genic enhancers	Brain Cingulate Gyrus	brain
47	chr2:54860400-54862400	Enhancers	HUVEC	blood vessel
48	chr2:54860400-54863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:54860400-54863800	Weak transcription	K562	blood
50	chr2:54860400-54864200	Genic enhancers	Fetal Muscle Leg	muscle

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