Variant report

Variant	rs2516634
Chromosome Location	chr11:62367186-62367187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:62366502-62367303	IMR90	lung:	n/a	n/a
2	POLR2A	chr11:62366105-62367187	HUVEC	blood vessel:	n/a	n/a
3	SP1	chr11:62366226-62367302	HCT-116	colon:	n/a	chr11:62366846-62366856 chr11:62366857-62366878 chr11:62367145-62367157 chr11:62366794-62366805 chr11:62367146-62367155 chr11:62366846-62366856
4	MYBL2	chr11:62366457-62367230	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:62367137-62367193	HepG2	liver:	n/a	n/a
6	GATA1	chr11:62366744-62368510	PBDE	blood:	n/a	chr11:62368255-62368276 chr11:62368262-62368269 chr11:62367106-62367114 chr11:62368260-62368270 chr11:62367399-62367408 chr11:62368262-62368272 chr11:62368257-62368273 chr11:62368260-62368269
7	CHD1	chr11:62365894-62370422	IMR90	lung:	n/a	chr11:62369509-62369519 chr11:62368807-62368817 chr11:62368545-62368555
8	GATA3	chr11:62366331-62367327	A549	lung:	n/a	chr11:62367106-62367114
9	NFIC	chr11:62366244-62367244	ECC-1	luminal epithelium:	n/a	n/a
10	HCFC1	chr11:62366328-62367356	Hela-S3	cervix:	n/a	n/a
11	ATF2	chr11:62366565-62367225	GM12878	blood:	n/a	n/a
12	SP1	chr11:62366493-62367205	A549	lung:	n/a	chr11:62366846-62366856 chr11:62366857-62366878 chr11:62367145-62367157 chr11:62366794-62366805 chr11:62367146-62367155 chr11:62366846-62366856
13	PML	chr11:62366297-62367195	GM12878	blood:	n/a	n/a
14	MAX	chr11:62366569-62367189	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr11:62366106-62367198	HUVEC	blood vessel:	n/a	n/a
16	EBF1	chr11:62365930-62367760	GM12878	blood:	n/a	chr11:62366640-62366651
17	SP1	chr11:62366266-62367324	HCT-116	colon:	n/a	chr11:62366846-62366856 chr11:62366857-62366878 chr11:62367145-62367157 chr11:62366794-62366805 chr11:62367146-62367155 chr11:62366846-62366856
18	SP1	chr11:62366415-62367228	A549	lung:	n/a	chr11:62366846-62366856 chr11:62366857-62366878 chr11:62367145-62367157 chr11:62366794-62366805 chr11:62367146-62367155 chr11:62366846-62366856
19	WRNIP1	chr11:62366285-62367754	GM12878	blood:	n/a	n/a
20	TCF12	chr11:62366347-62367262	A549	lung:	n/a	n/a
21	NR2F2	chr11:62366402-62367249	K562	blood:	n/a	n/a
22	EP300	chr11:62366347-62367205	A549	lung:	n/a	chr11:62367077-62367091
23	POLR2A	chr11:62367176-62367228	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr11:62366141-62367865	GM12878	blood:	n/a	n/a
25	TEAD4	chr11:62366464-62367200	K562	blood:	n/a	n/a
26	MXI1	chr11:62366177-62370539	SK-N-SH	brain:	n/a	n/a
27	MAZ	chr11:62366184-62367762	IMR90	lung:	n/a	n/a
28	GABPA	chr11:62366486-62367201	SK-N-SH	brain:	n/a	chr11:62367150-62367159

No.	Distal block	Cell Line	Cell type
1	chr11:62366402..62370002-chr11:62419166..62421218,5	MCF-7	breast:
2	chr11:62365951..62369565-chr11:62622521..62625872,5	K562	blood:
3	chr11:62366839..62369029-chr11:62472927..62475049,2	MCF-7	breast:
4	chr11:62365424..62367728-chr11:62413589..62415522,2	K562	blood:
5	chr11:62366079..62370074-chr11:62386678..62390504,7	MCF-7	breast:
6	chr11:62340363..62343212-chr11:62365252..62369475,4	MCF-7	breast:
7	chr11:62362631..62371847-chr11:62427548..62442313,26	MCF-7	breast:
8	chr11:62366750..62367416-chr11:62379616..62380490,3	MCF-7	breast:
9	chr11:62367185..62372634-chr11:62607154..62610784,6	MCF-7	breast:
10	chr11:62365870..62369296-chr11:62605447..62609594,6	K562	blood:
11	chr11:62366145..62371000-chr11:62493302..62496531,6	K562	blood:
12	chr11:62366894..62368811-chr11:62572540..62574175,2	MCF-7	breast:
13	chr11:62365873..62371127-chr11:62605447..62611263,11	K562	blood:
14	chr11:62361223..62372590-chr11:62430599..62435389,30	K562	blood:
15	chr11:62366089..62368766-chr11:62475317..62477241,2	MCF-7	breast:
16	chr11:62365667..62370630-chr11:62493549..62497299,5	MCF-7	breast:
17	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
18	chr11:62365983..62370724-chr11:62412063..62418373,9	K562	blood:
19	chr11:62366955..62369844-chr11:62535933..62538904,2	K562	blood:
20	chr11:62365338..62373022-chr11:62621930..62625872,13	K562	blood:
21	chr11:62363464..62373052-chr11:62429645..62434985,23	K562	blood:
22	chr11:62344267..62349689-chr11:62366431..62369887,5	MCF-7	breast:
23	chr11:62365089..62370067-chr11:62436026..62441323,7	K562	blood:
24	chr11:62366910..62368974-chr11:62608295..62610836,2	MCF-7	breast:
25	chr11:62364986..62367408-chr11:62393044..62395358,2	MCF-7	breast:
26	chr11:62366689..62370631-chr11:62475430..62478411,3	MCF-7	breast:
27	chr11:62365885..62368421-chr11:62552476..62555212,3	K562	blood:
28	chr11:62367022..62370613-chr11:62412660..62415093,5	MCF-7	breast:
29	chr11:62367086..62370916-chr11:62552894..62556677,4	MCF-7	breast:

Variant related genes	Relation type
MTA2	TF binding region
ENSG00000255508	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000149489	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000162227	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1061093	0.89[EUR][1000 genomes]
rs11231138	0.85[EUR][1000 genomes]
rs11231141	0.89[EUR][1000 genomes]
rs11231144	0.89[EUR][1000 genomes]
rs11231145	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231150	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231151	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11231152	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231154	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231155	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231156	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231161	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11553576	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12049914	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12223627	0.88[ASN][1000 genomes]
rs12225213	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12226821	0.88[ASN][1000 genomes]
rs12808829	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17773169	0.88[EUR][1000 genomes]
rs1801144	0.91[EUR][1000 genomes]
rs2428548	0.81[EUR][1000 genomes]
rs2428549	0.81[EUR][1000 genomes]
rs2428551	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2509961	0.81[EUR][1000 genomes]
rs2509967	0.81[EUR][1000 genomes]
rs2512562	0.81[EUR][1000 genomes]
rs2512563	0.81[EUR][1000 genomes]
rs2516633	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2849030	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849031	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34065644	0.88[ASN][1000 genomes]
rs34894392	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880596	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3923805	0.81[ASN][1000 genomes]
rs58720921	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61296092	0.89[EUR][1000 genomes]
rs67308910	0.85[ASN][1000 genomes]
rs7124057	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71490390	0.88[EUR][1000 genomes]
rs71490392	0.84[EUR][1000 genomes]
rs71490394	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72927213	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928833	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7930896	0.88[EUR][1000 genomes]
rs7937146	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7943191	0.89[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2516634	EML3	cis	Esophagus Mucosa	GTEx
rs2516634	MTA2	cis	Esophagus Mucosa	GTEx
rs2516634	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs2516634	EEF1G	cis	multi-tissue	Pritchard
rs2516634	ROM1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62359800-62368200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62360200-62367200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:62360200-62367200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:62360400-62367400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:62364600-62367200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:62365000-62368000	Transcr. at gene 5' and 3'	Hela-S3	cervix
7	chr11:62365200-62368200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:62365400-62367200	Weak transcription	Small Intestine	intestine
9	chr11:62365400-62367400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr11:62365600-62367800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
11	chr11:62365800-62367200	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr11:62365800-62367400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:62366000-62367200	Genic enhancers	Fetal Muscle Leg	muscle
14	chr11:62366000-62367400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:62366000-62367400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:62366000-62367400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:62366000-62367400	Genic enhancers	Fetal Stomach	stomach
18	chr11:62366000-62368000	Weak transcription	Gastric	stomach
19	chr11:62366000-62368200	Transcr. at gene 5' and 3'	K562	blood
20	chr11:62366200-62367200	Enhancers	Fetal Lung	lung
21	chr11:62366200-62367400	Genic enhancers	H1 Cell Line	embryonic stem cell
22	chr11:62366200-62367400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr11:62366200-62367400	Genic enhancers	Fetal Intestine Small	intestine
24	chr11:62366200-62367400	Genic enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:62366200-62367600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:62366200-62367800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
27	chr11:62366200-62367800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
28	chr11:62366200-62367800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
29	chr11:62366200-62367800	Transcr. at gene 5' and 3'	NH-A	brain
30	chr11:62366200-62367800	Transcr. at gene 5' and 3'	Osteobl	bone
31	chr11:62366200-62368000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
32	chr11:62366200-62368200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
33	chr11:62366200-62368200	Transcr. at gene 5' and 3'	A549	lung
34	chr11:62366200-62368200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr11:62366200-62368400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr11:62366200-62368400	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr11:62366400-62367200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:62366400-62367200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:62366400-62367200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:62366400-62367200	Enhancers	Fetal Heart	heart
41	chr11:62366400-62367200	Active TSS	Fetal Kidney	kidney
42	chr11:62366400-62367400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:62366400-62367400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:62366400-62367400	Enhancers	Liver	Liver
45	chr11:62366400-62367400	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr11:62366400-62367400	Enhancers	Fetal Brain Male	brain
47	chr11:62366400-62367400	Enhancers	Stomach Mucosa	stomach
48	chr11:62366400-62367600	Enhancers	Aorta	Aorta
49	chr11:62366400-62367600	Flanking Active TSS	HepG2	liver
50	chr11:62366400-62367800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung

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