Variant report

Variant	rs13432302
Chromosome Location	chr2:54813938-54813939
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54811907..54814094-chr2:54855383..54857261,2	MCF-7	breast:
2	chr2:54811634..54814043-chr2:54850461..54852371,2	MCF-7	breast:
3	chr2:54796611..54799496-chr2:54810522..54814074,3	MCF-7	breast:
4	chr2:54807406..54809056-chr2:54812643..54814659,2	MCF-7	breast:
5	chr2:54789199..54791941-chr2:54810651..54814148,3	K562	blood:
6	chr2:54764181..54766561-chr2:54813594..54815881,2	K562	blood:
7	chr2:54804194..54805987-chr2:54812413..54815195,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

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

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54802000-54816400	Enhancers	Liver	Liver
2	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
3	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:54804600-54814600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:54805400-54815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:54805600-54819800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:54807200-54814600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:54807200-54814800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:54807200-54815800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:54807200-54816400	Weak transcription	Aorta	Aorta
13	chr2:54807200-54819800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:54807800-54816200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:54807800-54818800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:54808400-54816800	Enhancers	Brain Anterior Caudate	brain
17	chr2:54808800-54815800	Weak transcription	Placenta	Placenta
18	chr2:54808800-54822800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:54809200-54814800	Genic enhancers	A549	lung
20	chr2:54809400-54815600	Weak transcription	Fetal Kidney	kidney
21	chr2:54809400-54816200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:54809400-54816400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:54809400-54816400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:54809400-54816400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr2:54809400-54821600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:54809600-54814000	Enhancers	Primary B cells from cord blood	blood
27	chr2:54809600-54814600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:54809600-54815200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:54809600-54815600	Weak transcription	Gastric	stomach
30	chr2:54809600-54816200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
32	chr2:54810000-54816400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr2:54810400-54814600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:54810400-54814600	Weak transcription	Lung	lung
35	chr2:54810400-54814800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:54810400-54815800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:54810400-54816400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:54810600-54815600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:54810800-54814000	Enhancers	Primary B cells from peripheral blood	blood
40	chr2:54810800-54814400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:54810800-54815200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:54810800-54815400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:54810800-54815600	Weak transcription	Colonic Mucosa	Colon
44	chr2:54811000-54814800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:54811000-54815600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:54811000-54815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:54811200-54816400	Enhancers	Hela-S3	cervix
48	chr2:54811400-54815200	Enhancers	K562	blood
49	chr2:54811400-54816400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:54811400-54816400	Enhancers	Fetal Thymus	thymus

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