Variant report

Variant	rs72927237
Chromosome Location	chr11:62381483-62381484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:62381382-62381697	T-47D	breast:	n/a	n/a
2	POLR2A	chr11:62379125-62381560	GM12892	blood:	n/a	n/a
3	GATA3	chr11:62381339-62381712	T-47D	breast:	n/a	chr11:62381360-62381370
4	POLR2A	chr11:62379143-62381515	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr11:62378851-62381521	K562	blood:	n/a	n/a
6	POLR2A	chr11:62380597-62381555	GM12891	blood:	n/a	n/a
7	ZNF263	chr11:62381092-62382420	HEK293-T-REx	kidney:	n/a	chr11:62382000-62382009 chr11:62381372-62381381 chr11:62382002-62382023 chr11:62381369-62381378 chr11:62382016-62382025 chr11:62381375-62381384 chr11:62381366-62381375
8	POLR2A	chr11:62380884-62381592	K562	blood:	n/a	n/a
9	HCFC1	chr11:62378961-62382383	Hela-S3	cervix:	n/a	n/a
10	MAX	chr11:62381457-62382347	HCT-116	colon:	n/a	n/a
11	MAFK	chr11:62381421-62382106	HepG2	liver:	n/a	chr11:62381978-62381987
12	POLR2A	chr11:62378999-62381495	GM12878	blood:	n/a	n/a
13	MAFF	chr11:62381468-62381668	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:62378894-62382468	K562	blood:	n/a	n/a
15	POLR2A	chr11:62381446-62382296	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr11:62380274-62382136	HepG2	liver:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62341571..62343456-chr11:62380691..62382479,2	MCF-7	breast:
2	chr11:62379075..62382019-chr11:62621736..62623514,2	K562	blood:
3	chr11:62377281..62381950-chr11:62571197..62574724,7	K562	blood:
4	chr11:62381071..62383567-chr11:62400385..62403576,3	K562	blood:
5	chr11:62160287..62162043-chr11:62381088..62384436,3	K562	blood:
6	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
7	chr11:62377695..62382560-chr11:62411978..62415698,6	MCF-7	breast:
8	chr11:62378127..62383239-chr11:62606559..62611171,5	K562	blood:
9	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
10	chr11:62379585..62382197-chr11:62420262..62422410,4	MCF-7	breast:
11	chr11:62381310..62383705-chr11:62395490..62397598,2	K562	blood:
12	chr11:62355644..62361752-chr11:62377047..62383949,17	MCF-7	breast:
13	chr11:62378641..62383731-chr11:62412268..62415992,8	K562	blood:
14	chr11:62379447..62382071-chr11:62443592..62448263,4	K562	blood:
15	chr11:62375885..62391030-chr11:62428132..62435550,30	MCF-7	breast:
16	chr11:62378127..62382168-chr11:62606723..62610399,5	MCF-7	breast:
17	chr11:62378832..62381851-chr11:62418002..62421701,6	K562	blood:
18	chr11:62379544..62381824-chr11:62648377..62649944,2	MCF-7	breast:
19	chr11:62379829..62381950-chr11:62572361..62574318,2	K562	blood:
20	chr11:62379915..62385772-chr11:62411575..62415305,8	MCF-7	breast:
21	chr11:62379764..62382350-chr11:62493558..62496251,2	MCF-7	breast:
22	chr11:62380126..62381894-chr11:62493421..62495399,2	MCF-7	breast:
23	chr11:62379189..62381832-chr11:62393317..62395975,2	MCF-7	breast:
24	chr11:62379239..62383319-chr11:62411576..62416139,7	K562	blood:
25	chr11:62377568..62383566-chr11:62416977..62422354,8	K562	blood:
26	chr11:62379447..62382071-chr11:62444982..62448263,3	K562	blood:
27	chr11:62378061..62382695-chr11:62418790..62422319,4	MCF-7	breast:
28	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:
29	chr11:62378763..62382397-chr11:62538915..62541537,3	K562	blood:

No data

Variant related genes	Relation type
EML3	TF binding region
ENSG00000255126	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000162194	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11231150	0.80[ASN][1000 genomes]
rs11231152	0.80[ASN][1000 genomes]
rs11231154	0.86[ASN][1000 genomes]
rs11231156	0.86[ASN][1000 genomes]
rs12049914	0.86[ASN][1000 genomes]
rs12223627	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12225213	0.82[ASN][1000 genomes]
rs12226821	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1801144	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2516633	0.85[EUR][1000 genomes]
rs34065644	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923805	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60098285	0.81[AMR][1000 genomes]
rs67308910	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7122950	0.85[EUR][1000 genomes]
rs71490394	0.86[ASN][1000 genomes]
rs72927213	0.86[ASN][1000 genomes]
rs7942154	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7942991	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
6	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
7	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
8	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
9	nsv897622	chr11:62366986-62392229	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs72927237	EML3	cis	Whole Blood	GTEx
rs72927237	MTA2	cis	Esophagus Mucosa	GTEx
rs72927237	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62379800-62381800	Weak transcription	Primary T cells from cord blood	blood
2	chr11:62379800-62384200	Weak transcription	Fetal Lung	lung
3	chr11:62380000-62386600	Weak transcription	GM12878-XiMat	blood
4	chr11:62380200-62383800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:62380400-62382600	Enhancers	NHEK	skin
6	chr11:62380400-62384200	Weak transcription	Aorta	Aorta
7	chr11:62380400-62386600	Weak transcription	HSMMtube	muscle
8	chr11:62380600-62382000	Enhancers	Placenta	Placenta
9	chr11:62380600-62382000	Genic enhancers	NHLF	lung
10	chr11:62380600-62382200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr11:62380600-62382400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:62380600-62382400	Enhancers	Stomach Mucosa	stomach
13	chr11:62380600-62382400	Enhancers	HMEC	breast
14	chr11:62380600-62382600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr11:62380600-62382600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:62380600-62382800	Weak transcription	Ovary	ovary
17	chr11:62380600-62387800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:62380600-62388000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:62380600-62388000	Weak transcription	Psoas Muscle	Psoas
20	chr11:62380600-62388200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:62380600-62388400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:62380800-62381600	Enhancers	Colonic Mucosa	Colon
23	chr11:62380800-62381600	Weak transcription	Thymus	Thymus
24	chr11:62380800-62381800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr11:62380800-62382000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr11:62380800-62382000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:62380800-62382000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:62380800-62382000	Enhancers	Liver	Liver
29	chr11:62380800-62382000	Enhancers	Duodenum Mucosa	Duodenum
30	chr11:62380800-62382000	Weak transcription	Fetal Stomach	stomach
31	chr11:62380800-62382000	Enhancers	Gastric	stomach
32	chr11:62380800-62382200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:62380800-62382200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:62380800-62382200	Enhancers	Esophagus	oesophagus
35	chr11:62380800-62382400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr11:62380800-62382400	Enhancers	A549	lung
37	chr11:62380800-62382600	Enhancers	Fetal Intestine Large	intestine
38	chr11:62380800-62382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:62380800-62382800	Weak transcription	Dnd41	blood
40	chr11:62380800-62383000	Enhancers	K562	blood
41	chr11:62380800-62383800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:62380800-62383800	Weak transcription	Small Intestine	intestine
43	chr11:62380800-62384000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr11:62380800-62384000	Weak transcription	Primary B cells from cord blood	blood
45	chr11:62380800-62387800	Weak transcription	HSMM	muscle
46	chr11:62380800-62388200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:62380800-62388200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:62380800-62388400	Weak transcription	Right Atrium	heart
49	chr11:62381000-62381600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr11:62381000-62381800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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