Variant report

Variant	rs13021606
Chromosome Location	chr2:54829270-54829271
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10176359	0.92[EUR][1000 genomes]
rs10183043	0.84[EUR][1000 genomes]
rs10210502	0.86[EUR][1000 genomes]
rs10528	0.91[EUR][1000 genomes]
rs11555856	0.96[EUR][1000 genomes]
rs11892236	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11896957	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11902659	0.92[EUR][1000 genomes]
rs11904679	0.90[EUR][1000 genomes]
rs12713262	0.83[EUR][1000 genomes]
rs12713263	0.83[EUR][1000 genomes]
rs12713270	0.96[EUR][1000 genomes]
rs12713271	0.96[EUR][1000 genomes]
rs12713272	0.92[EUR][1000 genomes]
rs12713273	0.87[EUR][1000 genomes]
rs12987967	0.88[EUR][1000 genomes]
rs13004944	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13021615	0.81[EUR][1000 genomes]
rs13391803	0.89[EUR][1000 genomes]
rs13408295	0.86[EUR][1000 genomes]
rs17039558	0.87[EUR][1000 genomes]
rs17046036	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17046061	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17046067	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17046077	0.82[EUR][1000 genomes]
rs17046108	0.83[EUR][1000 genomes]
rs2229503	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2271329	0.82[EUR][1000 genomes]
rs34077590	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34094680	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34308676	0.85[EUR][1000 genomes]
rs34311770	0.89[EUR][1000 genomes]
rs34978408	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35619551	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3739109	0.81[EUR][1000 genomes]
rs3796022	0.82[EUR][1000 genomes]
rs4261758	0.83[EUR][1000 genomes]
rs4358162	0.96[EUR][1000 genomes]
rs4519566	0.88[EUR][1000 genomes]
rs4577321	0.88[EUR][1000 genomes]
rs57281248	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58419243	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61126015	0.85[EUR][1000 genomes]
rs6545430	0.84[EUR][1000 genomes]
rs6545435	0.88[EUR][1000 genomes]
rs66693131	0.82[EUR][1000 genomes]
rs67079536	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6721612	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6724136	0.84[EUR][1000 genomes]
rs67244067	0.94[EUR][1000 genomes]
rs6730876	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6734445	0.85[EUR][1000 genomes]
rs6734536	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6741053	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72806653	0.83[EUR][1000 genomes]
rs7424459	0.91[EUR][1000 genomes]
rs7569127	0.92[EUR][1000 genomes]
rs7584223	0.88[EUR][1000 genomes]
rs7586066	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7591204	0.92[ASN][1000 genomes]
rs7602992	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs13021606	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:54822200-54833800	Genic enhancers	HepG2	liver
4	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
5	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
6	chr2:54822400-54834000	Enhancers	Right Atrium	heart
7	chr2:54822800-54831600	Genic enhancers	A549	lung
8	chr2:54823200-54831000	Genic enhancers	Fetal Intestine Large	intestine
9	chr2:54823800-54829400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:54824000-54829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:54824200-54829600	Enhancers	Fetal Heart	heart
12	chr2:54824200-54830600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:54824800-54829600	Genic enhancers	Primary hematopoietic stem cells	blood
16	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:54825000-54829800	Weak transcription	Fetal Brain Male	brain
19	chr2:54825800-54829600	Genic enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:54826000-54829600	Genic enhancers	Fetal Thymus	thymus
21	chr2:54826000-54831200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:54826400-54830200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:54826600-54832000	Genic enhancers	Fetal Intestine Small	intestine
24	chr2:54826800-54829600	Genic enhancers	Fetal Lung	lung
25	chr2:54826800-54830200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:54826800-54834400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr2:54827000-54829400	Enhancers	HSMMtube	muscle
28	chr2:54827000-54829600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:54827200-54830000	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr2:54827200-54830400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:54827200-54832200	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:54827200-54833800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:54827200-54834000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
35	chr2:54827400-54830200	Weak transcription	Thymus	Thymus
36	chr2:54827400-54831000	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:54827400-54832000	Weak transcription	Brain Germinal Matrix	brain
38	chr2:54827400-54832000	Weak transcription	Fetal Brain Female	brain
39	chr2:54827600-54829400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:54827600-54829400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:54827600-54829400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:54827600-54829400	Weak transcription	Esophagus	oesophagus
43	chr2:54827600-54829400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:54827600-54829600	Weak transcription	Placenta	Placenta
45	chr2:54827600-54829600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr2:54827600-54829600	Enhancers	K562	blood
47	chr2:54827600-54830600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:54827600-54830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:54827600-54830800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:54827600-54831200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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