Variant report

Variant	rs489778
Chromosome Location	chr11:62437647-62437648
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:122)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 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	RCOR1	chr11:62436478-62437723	K562	blood:	n/a	n/a
4	GATA3	chr11:62437466-62437790	T-47D	breast:	n/a	n/a
5	STAT3	chr11:62437634-62437816	MCF10A-Er-Src	breast:	n/a	n/a
6	TEAD4	chr11:62436575-62438170	K562	blood:	n/a	n/a
7	POLR2A	chr11:62436886-62437821	HCT-116	colon:	n/a	n/a
8	POLR2A	chr11:62437505-62438072	U87	brain:	n/a	n/a
9	POLR2A	chr11:62436872-62437870	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr11:62436600-62437812	K562	blood:	n/a	n/a
11	POLR2A	chr11:62437519-62437901	U87	brain:	n/a	n/a
12	POLR2A	chr11:62436833-62437782	HL-60	blood:	n/a	n/a
13	POLR2A	chr11:62436579-62437718	ECC-1	luminal epithelium:	n/a	n/a
14	TAL1	chr11:62437439-62437777	K562	blood:	n/a	n/a
15	POLR2A	chr11:62437407-62437711	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr11:62436898-62437845	K562	blood:	n/a	n/a
17	POLR2A	chr11:62437312-62437854	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr11:62436917-62437830	ECC-1	luminal epithelium:	n/a	n/a
19	UBTF	chr11:62437561-62437647	K562	blood:	n/a	n/a
20	POLR2A	chr11:62436847-62437806	MCF-7	breast:	n/a	n/a
21	POLR2A	chr11:62436207-62438036	K562	blood:	n/a	n/a
22	POLR2A	chr11:62431933-62437819	HepG2	liver:	n/a	n/a
23	POLR2A	chr11:62432041-62438244	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr11:62436702-62440623	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr11:62436944-62437652	U87	brain:	n/a	n/a
26	TCF12	chr11:62436862-62437671	A549	lung:	n/a	chr11:62436959-62436966
27	POLR2A	chr11:62437215-62437700	GM12892	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:62437615-62437665	NH-A	brain:	n/a
2	chr11:62437636-62437686	BJ	skin:	n/a
3	chr11:62437615-62437665	MCF10A-Er-Src	breast:	n/a
4	chr11:62437636-62437686	PANC-1	pancreas:	n/a
5	chr11:62437636-62437686	HRE	kidney:	n/a
6	chr11:62437636-62437686	GM12878	blood:	n/a
7	chr11:62437636-62437686	HCT-116	colon:	n/a
8	chr11:62437615-62437665	BE2_C	brain:	n/a
9	chr11:62437615-62437665	Hela-S3	cervix:	n/a
10	chr11:62437636-62437686	HCPEpiC	choroid plexus:	n/a
11	chr11:62437615-62437665	Hepatocyte	liver:	n/a
12	chr11:62437636-62437686	HAEpiC	amniotic membrane:	n/a
13	chr11:62437615-62437665	AoSMC	blood vessel:	n/a
14	chr11:62437615-62437665	IMR90	lung:	fetal
15	chr11:62437636-62437686	IMR90	lung:	fetal
16	chr11:62437636-62437686	PFSK-1	brain:	n/a
17	chr11:62437636-62437686	H1-hESC	embryonic stem cell:	embryo
18	chr11:62437636-62437686	MCF10A-Er-Src	breast:	n/a
19	chr11:62437615-62437665	GM12878	blood:	n/a
20	chr11:62437615-62437665	SK-N-MC	brain:	n/a
21	chr11:62437615-62437665	GM19239	blood:	n/a
22	chr11:62437636-62437686	HEEpiC	esophagus:	n/a
23	chr11:62437615-62437665	PANC-1	pancreas:	n/a
24	chr11:62437636-62437686	GM06990	blood:	n/a
25	chr11:62437636-62437686	T-47D	breast:	n/a
26	chr11:62437636-62437686	Hela-S3	cervix:	n/a
27	chr11:62437636-62437686	MCF-7	breast:	n/a
28	chr11:62437615-62437665	HCT-116	colon:	n/a
29	chr11:62437636-62437686	Jurkat	blood:	n/a
30	chr11:62437615-62437665	GM06990	blood:	n/a
31	chr11:62437636-62437686	SK-N-SH	brain:	n/a
32	chr11:62437615-62437665	HRE	kidney:	n/a
33	chr11:62437636-62437686	A549	lung:	n/a
34	chr11:62437615-62437665	T-47D	breast:	n/a
35	chr11:62437636-62437686	HCF	heart:	n/a
36	chr11:62437636-62437686	HUVEC	blood vessel:	n/a
37	chr11:62437615-62437665	HCPEpiC	choroid plexus:	n/a
38	chr11:62437615-62437665	Jurkat	blood:	n/a
39	chr11:62437636-62437686	AoSMC	blood vessel:	n/a
40	chr11:62437615-62437665	RPTEC	kidney:	n/a
41	chr11:62437615-62437665	HRPEpiC	eye:	n/a
42	chr11:62437615-62437665	HMEC	breast:	n/a
43	chr11:62437615-62437665	HUVEC	blood vessel:	n/a
44	chr11:62437615-62437665	CMK	blood:	n/a
45	chr11:62437615-62437665	ovcar-3	ovarian:	n/a
46	chr11:62437615-62437665	SK-N-SH_RA	brain:	n/a
47	chr11:62437615-62437665	SAEC	small airway:	n/a
48	chr11:62437615-62437665	NHDF-neo	bronchial:	n/a
49	chr11:62437615-62437665	HRCEpiC	kidney:	n/a
50	chr11:62437636-62437686	NH-A	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr11:62431946..62440629-chr11:62523095..62533975,14	K562	blood:
2	chr11:62357027..62359159-chr11:62437466..62439059,2	MCF-7	breast:
3	chr11:62437407..62441142-chr11:62472174..62474632,6	K562	blood:
4	chr11:62385249..62394022-chr11:62430274..62439840,30	K562	blood:
5	chr11:62437394..62440869-chr11:62646713..62650476,3	MCF-7	breast:
6	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:
7	chr11:62431329..62439956-chr11:62534683..62540515,15	K562	blood:
8	chr11:62337874..62344185-chr11:62431132..62441783,22	K562	blood:
9	chr11:62436186..62443328-chr11:62605173..62609692,11	MCF-7	breast:
10	chr11:62437179..62441189-chr11:62491770..62496446,10	K562	blood:
11	chr11:62437536..62440497-chr11:62572086..62574546,2	K562	blood:
12	chr11:62436317..62438708-chr11:62474733..62477422,2	MCF-7	breast:
13	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
14	chr11:62378546..62380116-chr11:62436360..62439103,2	MCF-7	breast:
15	chr11:62365089..62370067-chr11:62436026..62441323,7	K562	blood:
16	chr11:62357319..62360814-chr11:62437164..62440854,7	K562	blood:
17	chr11:62359198..62361041-chr11:62437324..62439045,2	MCF-7	breast:
18	chr11:62437470..62440242-chr11:62620623..62623649,4	K562	blood:
19	chr11:62435729..62437858-chr11:62648872..62651709,3	K562	blood:
20	chr11:62430854..62442244-chr11:62606149..62611424,26	K562	blood:
21	chr11:62362631..62371847-chr11:62427548..62442313,26	MCF-7	breast:
22	chr11:62436416..62439082-chr11:62606884..62609041,4	MCF-7	breast:
23	chr11:62436644..62439359-chr11:62646545..62649165,3	MCF-7	breast:
24	chr11:62357319..62362043-chr11:62437125..62441010,6	K562	blood:
25	chr11:62437275..62439267-chr11:62553452..62555384,2	MCF-7	breast:
26	chr11:62362245..62364741-chr11:62437553..62440349,2	K562	blood:
27	chr11:62339758..62342411-chr11:62437279..62439132,3	MCF-7	breast:
28	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
29	chr11:62436333..62448417-chr11:62605662..62610542,19	K562	blood:
30	chr11:62429368..62441438-chr11:62488512..62498189,36	K562	blood:
31	chr11:62431330..62441336-chr11:62489515..62497875,29	MCF-7	breast:
32	chr11:62407005..62417562-chr11:62426315..62441135,36	MCF-7	breast:
33	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
34	chr11:62313199..62316159-chr11:62436456..62439298,3	MCF-7	breast:
35	chr11:62384891..62391618-chr11:62430274..62437661,19	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255432	TF binding region
C11orf83	TF binding region
C11orf48	TF binding region
C11orf48	CpG island
C11orf83	CpG island
ENSG00000255432	CpG island
ENSG00000133316	Chromatin interaction
ENSG00000149489	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000257058	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000162188	Chromatin interaction
ENSG00000168002	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000254964	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000255717	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10792355	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11231161	0.82[JPT][hapmap]
rs11231172	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231173	0.87[ASN][1000 genomes]
rs11231176	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs11231181	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231182	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231183	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231184	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12291465	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364753	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364756	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637597	0.91[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1893458	0.97[ASN][1000 genomes]
rs2849030	0.85[YRI][hapmap]
rs2849031	0.85[YRI][hapmap]
rs2956993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs2956995	0.85[AFR][1000 genomes];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]
rs3018561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs3809079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489748	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597259	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435036	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs644616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs661182	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67909703	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128852	0.81[ASN][1000 genomes]
rs71490396	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71490397	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7949030	1.00[CHB][hapmap];1.00[JPT][hapmap];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
rs489778	EML3	cis	Esophagus Mucosa	GTEx
rs489778	EML3	cis	uninvolved skin	skin_eQTL

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

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	chr11:62434600-62438400	Weak transcription	Fetal Kidney	kidney
4	chr11:62434800-62438000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:62434800-62438200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:62434800-62438400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:62434800-62438400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:62435200-62438000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:62435200-62438000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:62435200-62438000	Weak transcription	Fetal Brain Male	brain
11	chr11:62435200-62438000	Weak transcription	Fetal Brain Female	brain
12	chr11:62435200-62438200	Weak transcription	Brain Germinal Matrix	brain
13	chr11:62435200-62438200	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:62435200-62438400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:62435200-62438400	Weak transcription	Brain Anterior Caudate	brain
16	chr11:62435200-62438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:62435200-62438400	Weak transcription	Fetal Lung	lung
18	chr11:62435200-62438400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:62435200-62438400	Weak transcription	NHDF-Ad	bronchial
20	chr11:62435200-62438600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:62435200-62438600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:62435400-62438000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:62435400-62438400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:62435400-62438400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:62435400-62438400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:62435400-62438400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:62435400-62438400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:62435400-62438400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:62435400-62438400	Weak transcription	Small Intestine	intestine
30	chr11:62435600-62438000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:62435600-62438200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:62435600-62438200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:62435600-62438400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:62435600-62438400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:62435600-62438400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:62435600-62438400	Weak transcription	Primary T cells from cord blood	blood
37	chr11:62435600-62438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:62435600-62438400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:62435800-62438400	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:62435800-62438600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:62436400-62438200	Enhancers	Placenta	Placenta
42	chr11:62436800-62437800	Enhancers	Liver	Liver
43	chr11:62436800-62437800	Enhancers	Colonic Mucosa	Colon
44	chr11:62436800-62438400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr11:62437000-62437800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:62437000-62437800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr11:62437000-62437800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:62437000-62437800	Enhancers	Aorta	Aorta
49	chr11:62437000-62437800	Genic enhancers	Lung	lung
50	chr11:62437000-62437800	Enhancers	Psoas Muscle	Psoas

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