Variant report

Variant	rs12291465
Chromosome Location	chr11:62437000-62437001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62436600-62437835	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:62432024-62437817	K562	blood:	n/a	n/a
3	POLR2A	chr11:62436808-62437515	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:62436963-62437561	Raji	blood:	n/a	n/a
5	RCOR1	chr11:62436478-62437723	K562	blood:	n/a	n/a
6	YY1	chr11:62436901-62437168	K562	blood:	n/a	n/a
7	ZNF384	chr11:62436367-62437147	K562	blood:	n/a	n/a
8	MTA3	chr11:62436941-62437629	GM12878	blood:	n/a	n/a
9	TEAD4	chr11:62436575-62438170	K562	blood:	n/a	n/a
10	POLR2A	chr11:62436919-62437058	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr11:62436886-62437821	HCT-116	colon:	n/a	n/a
12	POLR2A	chr11:62436949-62437440	A549	lung:	n/a	n/a
13	POLR2A	chr11:62436863-62437202	U87	brain:	n/a	n/a
14	POLR2A	chr11:62436872-62437870	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:62436600-62437812	K562	blood:	n/a	n/a
16	RCOR1	chr11:62436536-62437153	K562	blood:	n/a	n/a
17	POLR2A	chr11:62436833-62437782	HL-60	blood:	n/a	n/a
18	POLR2A	chr11:62436579-62437718	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr11:62436833-62437349	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr11:62436898-62437845	K562	blood:	n/a	n/a
21	POLR2A	chr11:62436904-62437067	ProgFib	skin:	n/a	n/a
22	POLR2A	chr11:62436917-62437830	ECC-1	luminal epithelium:	n/a	n/a
23	YY1	chr11:62436584-62437156	K562	blood:	n/a	n/a
24	POLR2A	chr11:62436984-62437458	A549	lung:	n/a	n/a
25	POLR2A	chr11:62436847-62437806	MCF-7	breast:	n/a	n/a
26	POLR2A	chr11:62436986-62437584	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr11:62436207-62438036	K562	blood:	n/a	n/a
28	POLR2A	chr11:62431933-62437819	HepG2	liver:	n/a	n/a
29	POLR2A	chr11:62436722-62437616	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr11:62436914-62437420	HCT-116	colon:	n/a	n/a
31	POLR2A	chr11:62432041-62438244	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr11:62436702-62440623	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr11:62436944-62437652	U87	brain:	n/a	n/a
34	TCF12	chr11:62436862-62437671	A549	lung:	n/a	chr11:62436959-62436966
35	IRF1	chr11:62436729-62437094	K562	blood:	n/a	chr11:62436922-62436935

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62431946..62440629-chr11:62523095..62533975,14	K562	blood:
2	chr11:62435703..62437436-chr11:62479698..62482195,2	K562	blood:
3	chr11:62385249..62394022-chr11:62430274..62439840,30	K562	blood:
4	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:
5	chr11:62431329..62439956-chr11:62534683..62540515,15	K562	blood:
6	chr11:62337874..62344185-chr11:62431132..62441783,22	K562	blood:
7	chr11:62436186..62443328-chr11:62605173..62609692,11	MCF-7	breast:
8	chr11:62436317..62438708-chr11:62474733..62477422,2	MCF-7	breast:
9	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
10	chr11:62378546..62380116-chr11:62436360..62439103,2	MCF-7	breast:
11	chr11:62365089..62370067-chr11:62436026..62441323,7	K562	blood:
12	chr11:62367573..62370441-chr11:62435647..62437526,2	K562	blood:
13	chr11:62434402..62437145-chr11:62472661..62475418,2	K562	blood:
14	chr11:62399251..62404493-chr11:62430147..62437411,9	MCF-7	breast:
15	chr11:62430865..62437145-chr11:62471927..62479051,19	K562	blood:
16	chr11:62435525..62437530-chr11:62537501..62540267,2	K562	blood:
17	chr11:62435729..62437858-chr11:62648872..62651709,3	K562	blood:
18	chr11:62430854..62442244-chr11:62606149..62611424,26	K562	blood:
19	chr11:62362631..62371847-chr11:62427548..62442313,26	MCF-7	breast:
20	chr11:62337261..62342687-chr11:62431505..62437310,11	MCF-7	breast:
21	chr11:62436416..62439082-chr11:62606884..62609041,4	MCF-7	breast:
22	chr11:62436644..62439359-chr11:62646545..62649165,3	MCF-7	breast:
23	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
24	chr11:62436333..62448417-chr11:62605662..62610542,19	K562	blood:
25	chr11:62429368..62441438-chr11:62488512..62498189,36	K562	blood:
26	chr11:62432928..62437015-chr13:114471159..114475403,3	MCF-7	breast:
27	chr11:62432560..62437098-chr11:62470787..62476744,13	MCF-7	breast:
28	chr11:62431330..62441336-chr11:62489515..62497875,29	MCF-7	breast:
29	chr11:62407005..62417562-chr11:62426315..62441135,36	MCF-7	breast:
30	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
31	chr11:62313199..62316159-chr11:62436456..62439298,3	MCF-7	breast:
32	chr11:62384891..62391618-chr11:62430274..62437661,19	K562	blood:

No data

Variant related genes	Relation type
C11orf48	TF binding region
C11orf83	TF binding region
ENSG00000255432	TF binding region
ENSG00000168000	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000257058	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000168002	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000149489	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000162188	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000254964	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000162222	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10792355	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792356	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897289	0.92[ASN][1000 genomes]
rs11231172	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231173	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11231176	0.96[EUR][1000 genomes]
rs11231181	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231183	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231184	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12364753	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13941	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637597	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1893458	0.97[ASN][1000 genomes]
rs2956993	0.97[ASN][1000 genomes]
rs2956995	0.97[ASN][1000 genomes]
rs2957122	0.88[ASN][1000 genomes]
rs2958236	0.88[ASN][1000 genomes]
rs3017188	0.90[ASN][1000 genomes]
rs3017666	0.82[ASN][1000 genomes]
rs3809079	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489748	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489778	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597259	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435036	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661182	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67909703	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693698	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128852	0.81[ASN][1000 genomes]
rs71490396	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71490397	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7949030	0.92[ASN][1000 genomes]
rs9736354	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12291465	EML3	cis	Esophagus Mucosa	GTEx
rs12291465	B3GAT3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:171 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62433800-62438600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62434400-62438400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:62434600-62437000	Weak transcription	Aorta	Aorta
4	chr11:62434600-62437000	Weak transcription	Esophagus	oesophagus
5	chr11:62434600-62437200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:62434600-62438400	Weak transcription	Fetal Kidney	kidney
7	chr11:62434800-62437000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:62434800-62437200	Weak transcription	HSMM	muscle
9	chr11:62434800-62438000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:62434800-62438200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:62434800-62438400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:62434800-62438400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:62435000-62437000	Weak transcription	HSMMtube	muscle
14	chr11:62435000-62437400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:62435000-62437400	Weak transcription	Right Ventricle	heart
16	chr11:62435000-62437400	Enhancers	Stomach Mucosa	stomach
17	chr11:62435000-62437600	Weak transcription	Brain Substantia Nigra	brain
18	chr11:62435200-62437000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:62435200-62437000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:62435200-62437000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr11:62435200-62437000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:62435200-62437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:62435200-62437000	Weak transcription	Gastric	stomach
24	chr11:62435200-62437000	Weak transcription	Lung	lung
25	chr11:62435200-62437000	Weak transcription	Psoas Muscle	Psoas
26	chr11:62435200-62437000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:62435200-62437000	Weak transcription	Right Atrium	heart
28	chr11:62435200-62437000	Weak transcription	HMEC	breast
29	chr11:62435200-62437200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:62435200-62437200	Weak transcription	Adipose Nuclei	Adipose
31	chr11:62435200-62437200	Weak transcription	Ovary	ovary
32	chr11:62435200-62437400	Strong transcription	Fetal Stomach	stomach
33	chr11:62435200-62437600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:62435200-62438000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:62435200-62438000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:62435200-62438000	Weak transcription	Fetal Brain Male	brain
37	chr11:62435200-62438000	Weak transcription	Fetal Brain Female	brain
38	chr11:62435200-62438200	Weak transcription	Brain Germinal Matrix	brain
39	chr11:62435200-62438200	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:62435200-62438400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:62435200-62438400	Weak transcription	Brain Anterior Caudate	brain
42	chr11:62435200-62438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:62435200-62438400	Weak transcription	Fetal Lung	lung
44	chr11:62435200-62438400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:62435200-62438400	Weak transcription	NHDF-Ad	bronchial
46	chr11:62435200-62438600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:62435200-62438600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:62435400-62437000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:62435400-62437000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:62435400-62437000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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