Variant report

Variant	rs13391803
Chromosome Location	chr2:54800128-54800129
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54758614..54760270-chr2:54799626..54801180,2	MCF-7	breast:
2	chr2:54782556..54791633-chr2:54796824..54803982,19	MCF-7	breast:
3	chr2:54799047..54801001-chr2:54844688..54847061,2	MCF-7	breast:
4	chr2:54799809..54803669-chr2:54884381..54886305,3	MCF-7	breast:
5	chr2:54749018..54751873-chr2:54799647..54801248,2	MCF-7	breast:
6	chr2:54783962..54788714-chr2:54796833..54801765,9	K562	blood:
7	chr2:54759032..54761078-chr2:54799312..54800939,2	MCF-7	breast:
8	chr2:54793317..54796723-chr2:54797852..54801262,4	MCF-7	breast:
9	chr2:54799877..54801952-chr2:54808384..54810954,2	K562	blood:
10	chr2:54798938..54801134-chr2:54831623..54833818,2	K562	blood:
11	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10166844	0.95[ASN][1000 genomes]
rs10169439	0.90[CEU][hapmap]
rs10169954	0.93[ASN][1000 genomes]
rs10169975	0.91[ASN][1000 genomes]
rs10170066	0.95[ASN][1000 genomes]
rs10170355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10176359	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10176445	1.00[CHB][hapmap]
rs10182538	0.95[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10183043	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10184128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10187338	0.95[ASN][1000 genomes]
rs10188185	1.00[CHB][hapmap]
rs10188545	0.90[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10205410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10206143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10208225	0.95[ASN][1000 genomes]
rs10210502	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10528	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11555856	0.89[EUR][1000 genomes]
rs11892236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11892443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11896957	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11898032	0.92[ASN][1000 genomes]
rs11898033	0.92[ASN][1000 genomes]
rs11902659	0.89[EUR][1000 genomes]
rs11902987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11904679	0.85[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs12713262	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713263	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713264	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs12713265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12713266	0.95[ASN][1000 genomes]
rs12713267	0.92[ASN][1000 genomes]
rs12713268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12713269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12713270	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713271	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713272	0.89[EUR][1000 genomes]
rs12713273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713274	0.89[ASN][1000 genomes]
rs12987967	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13004944	0.83[EUR][1000 genomes]
rs13021606	0.89[EUR][1000 genomes]
rs13021615	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs13036147	0.80[EUR][1000 genomes]
rs13386146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13391522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13403284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13407214	0.97[ASN][1000 genomes]
rs13408295	0.83[EUR][1000 genomes]
rs13428703	0.85[CEU][hapmap]
rs13432302	0.95[ASN][1000 genomes]
rs17039558	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[EUR][1000 genomes]
rs17045939	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs17046036	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17046061	0.88[EUR][1000 genomes]
rs17046067	0.88[EUR][1000 genomes]
rs17046077	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs17046097	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17046108	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17046257	1.00[CHB][hapmap]
rs2048370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2229503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2271329	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs28581481	0.93[ASN][1000 genomes]
rs3287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34077590	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34094680	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34263579	0.82[EUR][1000 genomes]
rs34308676	0.90[EUR][1000 genomes]
rs34311770	0.88[EUR][1000 genomes]
rs34429083	0.81[EUR][1000 genomes]
rs34978408	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354232	0.88[CHB][hapmap]
rs35619551	0.87[EUR][1000 genomes]
rs36018286	0.80[EUR][1000 genomes]
rs3739109	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3796017	0.95[ASN][1000 genomes]
rs3796018	0.95[ASN][1000 genomes]
rs3796019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796022	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[EUR][1000 genomes]
rs4261758	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs4319969	0.86[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs4346422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4347868	0.92[ASN][1000 genomes]
rs4358162	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4374410	0.93[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4519566	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45487791	0.81[EUR][1000 genomes]
rs4577321	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4616509	0.95[ASN][1000 genomes]
rs4641979	0.95[ASN][1000 genomes]
rs57281248	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58419243	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61126015	0.88[EUR][1000 genomes]
rs6545430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs66693131	0.84[EUR][1000 genomes]
rs6706263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67079536	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6708082	0.85[CEU][hapmap]
rs6721612	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6724136	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67244067	0.91[EUR][1000 genomes]
rs6730876	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6734445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739140	0.92[ASN][1000 genomes]
rs6741053	0.85[EUR][1000 genomes]
rs6749802	0.92[ASN][1000 genomes]
rs6752720	0.85[CEU][hapmap]
rs72806653	0.84[EUR][1000 genomes]
rs7340302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7424459	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7564719	0.90[ASN][1000 genomes]
rs7569127	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7584223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7586066	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586311	0.95[ASN][1000 genomes]
rs7599241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7602992	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7608414	1.00[CHB][hapmap]
rs9677089	0.82[ASN][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
rs13391803	EML6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54789800-54801400	Enhancers	Liver	Liver
2	chr2:54791200-54801200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:54794400-54804200	Weak transcription	Ovary	ovary
4	chr2:54795200-54802200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:54795400-54801400	Enhancers	Fetal Thymus	thymus
6	chr2:54795600-54802400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr2:54795800-54801200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:54795800-54801800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr2:54795800-54801800	Enhancers	Fetal Kidney	kidney
10	chr2:54795800-54802400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:54795800-54803000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr2:54795800-54803200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:54795800-54803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr2:54796000-54801200	Enhancers	Thymus	Thymus
17	chr2:54796000-54801600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:54796000-54801600	Enhancers	Brain Substantia Nigra	brain
19	chr2:54796000-54801800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:54796000-54802000	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:54796000-54802000	Enhancers	Fetal Lung	lung
22	chr2:54796000-54802200	Enhancers	HSMMtube	muscle
23	chr2:54796000-54802400	Enhancers	Brain Hippocampus Middle	brain
24	chr2:54796000-54802600	Enhancers	HMEC	breast
25	chr2:54796000-54802800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr2:54796000-54804400	Enhancers	Adipose Nuclei	Adipose
27	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
28	chr2:54796200-54800400	Enhancers	Fetal Muscle Leg	muscle
29	chr2:54796200-54801400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:54796200-54801400	Enhancers	Placenta	Placenta
31	chr2:54796200-54801600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr2:54796200-54801800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr2:54796200-54806200	Enhancers	Right Atrium	heart
34	chr2:54796200-54806400	Enhancers	Brain Anterior Caudate	brain
35	chr2:54796200-54806800	Enhancers	Pancreas	Pancrea
36	chr2:54796400-54802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:54796400-54803600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:54796600-54801200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:54796600-54802200	Flanking Active TSS	GM12878-XiMat	blood
41	chr2:54796800-54800600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:54796800-54800600	Enhancers	Fetal Stomach	stomach
43	chr2:54796800-54802200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr2:54796800-54802800	Enhancers	K562	blood
45	chr2:54796800-54803200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:54796800-54806800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:54796800-54807400	Enhancers	Psoas Muscle	Psoas
48	chr2:54796800-54810200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:54796800-54810600	Enhancers	Small Intestine	intestine
50	chr2:54797200-54801000	Enhancers	Colon Smooth Muscle	Colon

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