Variant report

Variant	rs597259
Chromosome Location	chr11:62430659-62430660
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62352847..62362753-chr11:62430170..62436741,21	K562	blood:
2	chr11:62361223..62372590-chr11:62430599..62435389,30	K562	blood:
3	chr11:62385249..62394022-chr11:62430274..62439840,30	K562	blood:
4	chr11:62430414..62433224-chr15:49912377..49914448,2	MCF-7	breast:
5	chr11:62159712..62162875-chr11:62430303..62433825,3	MCF-7	breast:
6	chr11:62363464..62373052-chr11:62429645..62434985,23	K562	blood:
7	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:
8	chr11:62429885..62432914-chr11:62489795..62492762,3	K562	blood:
9	chr11:62429723..62431698-chr11:62622205..62624019,2	K562	blood:
10	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
11	chr11:62396393..62398543-chr11:62429250..62431703,2	MCF-7	breast:
12	chr11:62358185..62362116-chr11:62430559..62435536,12	MCF-7	breast:
13	chr11:62399251..62404493-chr11:62430147..62437411,9	MCF-7	breast:
14	chr11:62338989..62347081-chr11:62430108..62436394,14	MCF-7	breast:
15	chr11:62362631..62371847-chr11:62427548..62442313,26	MCF-7	breast:
16	chr11:62375885..62391030-chr11:62428132..62435550,30	MCF-7	breast:
17	chr11:62391837..62397393-chr11:62429147..62436074,7	K562	blood:
18	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
19	chr11:62429368..62441438-chr11:62488512..62498189,36	K562	blood:
20	chr11:62407005..62417562-chr11:62426315..62441135,36	MCF-7	breast:
21	chr11:62384891..62391618-chr11:62430274..62437661,19	K562	blood:

No data

Variant related genes	Relation type
ENSG00000149480	Chromatin interaction
ENSG00000149489	Chromatin interaction
ENSG00000166262	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000254964	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000104047	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000255126	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10792355	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897289	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11231161	1.00[JPT][hapmap]
rs11231172	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231173	0.87[ASN][1000 genomes]
rs11231176	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs11231181	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231182	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231183	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231184	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12291465	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364753	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364756	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13941	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637597	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1893458	0.97[ASN][1000 genomes]
rs2956993	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];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]
rs3018561	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3809079	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489748	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489778	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	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs644616	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs661182	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67909703	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693698	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128852	0.81[ASN][1000 genomes]
rs71490396	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71490397	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7949030	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs597259	EML3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62420800-62431600	Weak transcription	Small Intestine	intestine
2	chr11:62421200-62431600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:62421200-62431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:62421200-62431600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:62421200-62431600	Weak transcription	NHDF-Ad	bronchial
6	chr11:62421200-62432000	Weak transcription	Aorta	Aorta
7	chr11:62421200-62432000	Weak transcription	Brain Substantia Nigra	brain
8	chr11:62421200-62432000	Weak transcription	Esophagus	oesophagus
9	chr11:62421200-62432000	Weak transcription	Ovary	ovary
10	chr11:62421200-62432000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:62421400-62431400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:62421400-62431600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:62421400-62431600	Weak transcription	Brain Germinal Matrix	brain
14	chr11:62421400-62431600	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:62421400-62431600	Weak transcription	Fetal Kidney	kidney
16	chr11:62421400-62431600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:62421400-62431600	Weak transcription	HUVEC	blood vessel
18	chr11:62421400-62431800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:62421400-62431800	Weak transcription	Psoas Muscle	Psoas
20	chr11:62421400-62431800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:62421400-62432000	Weak transcription	Pancreas	Pancrea
22	chr11:62421800-62431400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:62422000-62431400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:62427800-62430800	Strong transcription	Fetal Intestine Large	intestine
25	chr11:62427800-62431000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:62428200-62431000	Strong transcription	Fetal Intestine Small	intestine
27	chr11:62428400-62430800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:62428400-62431000	Strong transcription	Fetal Stomach	stomach
29	chr11:62428600-62430800	Strong transcription	Fetal Thymus	thymus
30	chr11:62428800-62430800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:62428800-62431000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:62429000-62430800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:62429000-62430800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:62429000-62430800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:62429000-62430800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr11:62429000-62430800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:62429000-62430800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:62429000-62430800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:62429000-62430800	Strong transcription	Liver	Liver
40	chr11:62429000-62430800	Strong transcription	Fetal Brain Female	brain
41	chr11:62429000-62430800	Strong transcription	Placenta	Placenta
42	chr11:62429000-62430800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr11:62429000-62431000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:62429000-62431000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:62429000-62431000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:62429000-62431000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:62429000-62431000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:62429200-62430800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr11:62429200-62430800	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:62429200-62431000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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