Variant report

Variant	rs34894392
Chromosome Location	chr11:62374821-62374822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62373812-62380351	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
2	chr11:62374466..62376274-chr11:62412386..62414477,2	MCF-7	breast:
3	chr11:62357123..62359265-chr11:62373125..62375014,2	MCF-7	breast:
4	chr11:62371312..62376313-chr11:62493293..62497173,4	MCF-7	breast:
5	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
6	chr11:62374418..62378633-chr11:62387946..62390795,5	MCF-7	breast:
7	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
8	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:

No data

Variant related genes	Relation type
ROM1	TF binding region
EML3	TF binding region
ENSG00000162194	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000255508	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1061093	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11231138	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231141	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11231144	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11231145	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11231150	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231151	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11231152	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231154	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231155	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231156	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231161	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11553576	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12049914	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12223627	0.88[ASN][1000 genomes]
rs12225213	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12226821	0.88[ASN][1000 genomes]
rs12808829	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17773169	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1801144	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2428551	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2516633	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516634	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849030	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849031	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34065644	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35880596	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3923805	0.81[ASN][1000 genomes]
rs58720921	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61296092	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67308910	0.85[ASN][1000 genomes]
rs7124057	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71490390	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71490392	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71490394	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72927213	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928833	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7930896	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7937146	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7943191	0.86[AMR][1000 genomes];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34894392	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs34894392	EML3	cis	Esophagus Mucosa	GTEx
rs34894392	MTA2	cis	Esophagus Mucosa	GTEx
rs34894392	EEF1G	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62370000-62375200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:62370000-62378800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:62370200-62375000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:62370200-62379000	Weak transcription	Fetal Kidney	kidney
5	chr11:62370600-62375800	Weak transcription	NHEK	skin
6	chr11:62370600-62377200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:62370600-62378000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:62370600-62378600	Weak transcription	Small Intestine	intestine
9	chr11:62370600-62378800	Weak transcription	HSMMtube	muscle
10	chr11:62370800-62375000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr11:62370800-62375000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:62370800-62375000	Weak transcription	HSMM	muscle
13	chr11:62370800-62375200	Weak transcription	Brain Substantia Nigra	brain
14	chr11:62370800-62375200	Weak transcription	NH-A	brain
15	chr11:62370800-62375400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:62370800-62375600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:62370800-62375800	Weak transcription	Brain Angular Gyrus	brain
18	chr11:62370800-62377800	Strong transcription	Primary T cells from cord blood	blood
19	chr11:62370800-62378000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:62370800-62378000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:62370800-62378000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:62370800-62378400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:62370800-62378400	Weak transcription	Left Ventricle	heart
24	chr11:62370800-62378600	Weak transcription	Psoas Muscle	Psoas
25	chr11:62370800-62378600	Weak transcription	Right Atrium	heart
26	chr11:62371000-62375000	Weak transcription	NHDF-Ad	bronchial
27	chr11:62371000-62375200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr11:62371000-62376800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:62371000-62377000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:62371000-62378200	Strong transcription	Thymus	Thymus
31	chr11:62371000-62378400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:62371000-62378600	Strong transcription	Osteobl	bone
33	chr11:62371000-62378800	Weak transcription	Brain Germinal Matrix	brain
34	chr11:62371000-62379000	Weak transcription	Fetal Brain Female	brain
35	chr11:62371200-62375600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr11:62371200-62377400	Strong transcription	Lung	lung
37	chr11:62371200-62378200	Strong transcription	Placenta	Placenta
38	chr11:62371200-62378400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:62371400-62375200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:62371400-62376400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:62371400-62377600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:62371400-62378200	Strong transcription	Fetal Stomach	stomach
43	chr11:62371400-62378200	Strong transcription	Gastric	stomach
44	chr11:62371400-62378400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:62371600-62375200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr11:62371600-62378200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:62371600-62378400	Weak transcription	Stomach Mucosa	stomach
48	chr11:62371600-62379000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr11:62371800-62375000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:62371800-62375000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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