Variant report

Variant	rs12808829
Chromosome Location	chr11:62378660-62378661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 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
2	CTCF	chr11:62378540-62378690	GM12873	blood:	n/a	n/a
3	ZBTB7A	chr11:62378513-62378728	K562	blood:	n/a	n/a
4	HMGN3	chr11:62378634-62379056	K562	blood:	n/a	n/a
5	POLR2A	chr11:62377907-62378762	K562	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62378551..62381260-chr11:62552189..62554776,3	K562	blood:
2	chr11:62377281..62381950-chr11:62571197..62574724,7	K562	blood:
3	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
4	chr11:62378546..62380116-chr11:62436360..62439103,2	MCF-7	breast:
5	chr11:62377842..62380816-chr11:62605555..62609086,5	K562	blood:
6	chr11:62377695..62382560-chr11:62411978..62415698,6	MCF-7	breast:
7	chr11:62378127..62383239-chr11:62606559..62611171,5	K562	blood:
8	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
9	chr11:62339264..62341444-chr11:62378101..62380412,2	MCF-7	breast:
10	chr11:62377585..62379687-chr11:62554018..62556330,2	K562	blood:
11	chr11:62378546..62380090-chr11:62458877..62460420,2	K562	blood:
12	chr11:62377536..62380529-chr11:62493370..62497128,3	K562	blood:
13	chr11:62355644..62361752-chr11:62377047..62383949,17	MCF-7	breast:
14	chr11:62378641..62383731-chr11:62412268..62415992,8	K562	blood:
15	chr11:62377060..62379469-chr11:62472700..62475103,2	K562	blood:
16	chr11:62375885..62391030-chr11:62428132..62435550,30	MCF-7	breast:
17	chr11:62378127..62382168-chr11:62606723..62610399,5	MCF-7	breast:
18	chr11:62312633..62315593-chr11:62378252..62381432,4	MCF-7	breast:
19	chr11:62376924..62380375-chr11:62537380..62541874,4	K562	blood:
20	chr11:62377568..62383566-chr11:62416977..62422354,8	K562	blood:
21	chr11:62378061..62382695-chr11:62418790..62422319,4	MCF-7	breast:
22	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:

No data

Variant related genes	Relation type
EML3	TF binding region
ROM1	TF binding region
ENSG00000257058	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000124942	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1061093	0.84[EUR][1000 genomes]
rs11231141	0.84[EUR][1000 genomes]
rs11231144	0.84[EUR][1000 genomes]
rs11231145	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11231150	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231151	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231152	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231154	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11231155	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231156	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11231161	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11553576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12049914	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12225213	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17773169	0.83[EUR][1000 genomes]
rs1801144	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2428551	0.84[EUR][1000 genomes]
rs2516633	0.88[ASN][1000 genomes]
rs2516634	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2849030	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2849031	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34894392	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35880596	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3923805	0.80[ASN][1000 genomes]
rs58720921	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61296092	0.84[EUR][1000 genomes]
rs67308910	0.80[AMR][1000 genomes]
rs7124057	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71490390	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71490394	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72927213	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7928833	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7930896	0.83[EUR][1000 genomes]
rs7937146	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7943191	0.82[AMR][1000 genomes];0.84[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
rs12808829	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs12808829	MTA2	cis	Esophagus Mucosa	GTEx
rs12808829	EML3	cis	Esophagus Mucosa	GTEx
rs12808829	EEF1G	cis	multi-tissue	Pritchard
rs12808829	EML3	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62370000-62378800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:62370200-62379000	Weak transcription	Fetal Kidney	kidney
3	chr11:62370600-62378800	Weak transcription	HSMMtube	muscle
4	chr11:62371000-62378800	Weak transcription	Brain Germinal Matrix	brain
5	chr11:62371000-62379000	Weak transcription	Fetal Brain Female	brain
6	chr11:62371600-62379000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:62371800-62378800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:62372600-62378800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:62374600-62379400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:62375200-62378800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr11:62375400-62379800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:62376000-62378800	Weak transcription	NH-A	brain
13	chr11:62376200-62378800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:62376200-62378800	Weak transcription	Aorta	Aorta
15	chr11:62376400-62378800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:62376400-62378800	Weak transcription	Brain Substantia Nigra	brain
17	chr11:62376800-62379000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:62377000-62378800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr11:62377000-62378800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:62377000-62378800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:62377000-62378800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr11:62377400-62379000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:62377600-62378800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:62377600-62378800	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr11:62377600-62378800	Enhancers	HUVEC	blood vessel
26	chr11:62377800-62378800	Genic enhancers	Adipose Nuclei	Adipose
27	chr11:62377800-62378800	Genic enhancers	Pancreas	Pancrea
28	chr11:62377800-62379200	Genic enhancers	Spleen	Spleen
29	chr11:62378000-62378800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:62378000-62378800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:62378000-62378800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr11:62378000-62378800	Genic enhancers	Esophagus	oesophagus
33	chr11:62378000-62378800	Genic enhancers	Right Ventricle	heart
34	chr11:62378000-62379000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:62378000-62379000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:62378000-62379000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:62378000-62379000	Genic enhancers	Fetal Muscle Leg	muscle
38	chr11:62378200-62378800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:62378200-62378800	Genic enhancers	Placenta	Placenta
40	chr11:62378200-62378800	Genic enhancers	Gastric	stomach
41	chr11:62378200-62378800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:62378200-62378800	Weak transcription	Thymus	Thymus
43	chr11:62378200-62378800	Enhancers	K562	blood
44	chr11:62378200-62379000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:62378200-62379000	Genic enhancers	Fetal Intestine Small	intestine
46	chr11:62378200-62379000	Enhancers	Fetal Lung	lung
47	chr11:62378200-62379000	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr11:62378200-62379000	Genic enhancers	Fetal Stomach	stomach
49	chr11:62378200-62379000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr11:62378400-62378800	Enhancers	H1 Cell Line	embryonic stem cell

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