Variant report

Variant	rs13399656
Chromosome Location	chr2:54802696-54802697
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54782556..54791633-chr2:54796824..54803982,19	MCF-7	breast:
2	chr2:54799809..54803669-chr2:54884381..54886305,3	MCF-7	breast:
3	chr2:54796760..54799671-chr2:54800450..54802770,2	K562	blood:
4	chr2:54795805..54798083-chr2:54801150..54802782,2	MCF-7	breast:
5	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10166844	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10169954	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10169975	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10170066	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10170355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10176359	1.00[CHB][hapmap]
rs10176445	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10182538	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10182836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10183043	0.93[ASN][1000 genomes]
rs10183867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10184128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187338	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10188185	1.00[CHB][hapmap]
rs10188545	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10193692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10205410	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10208225	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10210502	0.98[ASN][1000 genomes]
rs10528	1.00[CHB][hapmap]
rs1137645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892236	1.00[CHB][hapmap]
rs11892443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11896957	0.81[ASN][1000 genomes]
rs11898032	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11898033	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11902987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11904679	0.88[CHB][hapmap]
rs12713262	0.81[ASN][1000 genomes]
rs12713263	0.81[ASN][1000 genomes]
rs12713264	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713266	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713267	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713270	0.81[ASN][1000 genomes]
rs12713271	0.81[ASN][1000 genomes]
rs12713273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12713274	0.89[ASN][1000 genomes]
rs12987967	0.82[ASN][1000 genomes]
rs13021615	0.86[CHB][hapmap]
rs13386146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13403284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13407214	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423873	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13432302	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17039558	0.88[CHB][hapmap]
rs17045939	1.00[CHB][hapmap]
rs17046077	1.00[CHB][hapmap]
rs17046097	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs17046108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17046257	1.00[CHB][hapmap]
rs2048370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2229503	1.00[CHB][hapmap]
rs2271329	1.00[CHB][hapmap]
rs28581481	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34077590	0.93[ASN][1000 genomes]
rs34094680	0.87[ASN][1000 genomes]
rs34978408	0.81[ASN][1000 genomes]
rs354232	0.88[CHB][hapmap]
rs3739109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3796017	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796018	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs3796022	0.88[CHB][hapmap]
rs4261758	0.88[CHB][hapmap]
rs4319969	0.88[CHB][hapmap]
rs4346422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347868	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4358162	0.81[ASN][1000 genomes]
rs4374410	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4455200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519566	0.95[ASN][1000 genomes]
rs4577321	0.95[ASN][1000 genomes]
rs4616509	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641979	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57281248	0.93[ASN][1000 genomes]
rs6545430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6545435	1.00[CHB][hapmap]
rs6706263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6721612	0.81[ASN][1000 genomes]
rs6724136	0.85[ASN][1000 genomes]
rs6730876	0.81[ASN][1000 genomes]
rs6734445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6734536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6739140	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6740893	0.86[EUR][1000 genomes]
rs6749802	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7340302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424459	0.93[ASN][1000 genomes]
rs7556752	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7564719	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7569127	1.00[CHB][hapmap]
rs7584223	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7586066	0.97[ASN][1000 genomes]
rs7586311	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7591204	0.87[EUR][1000 genomes]
rs7591231	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7599241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602992	0.95[ASN][1000 genomes]
rs7608414	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs9677089	0.85[EUR][1000 genomes];0.85[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
rs13399656	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54794400-54804200	Weak transcription	Ovary	ovary
2	chr2:54795800-54803000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr2:54795800-54803200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:54795800-54803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr2:54796000-54802800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr2:54796000-54804400	Enhancers	Adipose Nuclei	Adipose
9	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
10	chr2:54796200-54806200	Enhancers	Right Atrium	heart
11	chr2:54796200-54806400	Enhancers	Brain Anterior Caudate	brain
12	chr2:54796200-54806800	Enhancers	Pancreas	Pancrea
13	chr2:54796400-54803600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:54796800-54802800	Enhancers	K562	blood
16	chr2:54796800-54803200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:54796800-54806800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:54796800-54807400	Enhancers	Psoas Muscle	Psoas
19	chr2:54796800-54810200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:54796800-54810600	Enhancers	Small Intestine	intestine
21	chr2:54797200-54805000	Enhancers	Spleen	Spleen
22	chr2:54797400-54808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:54797800-54807000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:54798600-54805600	Enhancers	NHDF-Ad	bronchial
25	chr2:54798800-54803000	Enhancers	Osteobl	bone
26	chr2:54798800-54806400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr2:54798800-54806600	Weak transcription	Fetal Brain Male	brain
28	chr2:54799200-54803000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:54799200-54803600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:54799400-54805000	Enhancers	Left Ventricle	heart
31	chr2:54799600-54803600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:54799800-54803000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:54800000-54803600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:54800000-54803800	Enhancers	Fetal Heart	heart
35	chr2:54800000-54807400	Enhancers	Right Ventricle	heart
36	chr2:54800200-54802800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:54800200-54803600	Enhancers	Fetal Intestine Small	intestine
38	chr2:54800200-54803800	Enhancers	Fetal Intestine Large	intestine
39	chr2:54800200-54805800	Enhancers	NHLF	lung
40	chr2:54800200-54806400	Enhancers	Stomach Mucosa	stomach
41	chr2:54800400-54803000	Enhancers	Stomach Smooth Muscle	stomach
42	chr2:54800400-54803200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr2:54800400-54805000	Genic enhancers	Fetal Muscle Leg	muscle
44	chr2:54800400-54805600	Genic enhancers	HSMM	muscle
45	chr2:54800600-54803600	Weak transcription	Fetal Stomach	stomach
46	chr2:54800600-54805400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:54800800-54802800	Enhancers	HUVEC	blood vessel
48	chr2:54800800-54803000	Transcr. at gene 5' and 3'	A549	lung
49	chr2:54800800-54803800	Weak transcription	Brain Germinal Matrix	brain
50	chr2:54800800-54804200	Weak transcription	Aorta	Aorta

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