Variant report

Variant	rs71490396
Chromosome Location	chr11:62429563-62429564
allele	A/T
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:7)
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	chr11:62428683-62429986	PFSK-1	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62396393..62398543-chr11:62429250..62431703,2	MCF-7	breast:
2	chr11:62362631..62371847-chr11:62427548..62442313,26	MCF-7	breast:
3	chr11:62375885..62391030-chr11:62428132..62435550,30	MCF-7	breast:
4	chr11:62391837..62397393-chr11:62429147..62436074,7	K562	blood:
5	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
6	chr11:62429368..62441438-chr11:62488512..62498189,36	K562	blood:
7	chr11:62407005..62417562-chr11:62426315..62441135,36	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA57	TF binding region
METTL12	TF binding region
ENSG00000149480	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000254964	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000149489	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10792355	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10792356	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231172	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231173	0.89[ASN][1000 genomes]
rs11231176	0.94[EUR][1000 genomes]
rs11231181	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11231182	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231183	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231184	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12291465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12364753	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12364756	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13941	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17637597	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809079	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4489748	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs489778	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs597259	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60435036	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs661182	0.87[EUR][1000 genomes]
rs67909703	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs693698	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71462310	0.80[EUR][1000 genomes]
rs71490397	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9736354	0.87[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
rs71490396	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62420800-62430200	Weak transcription	Gastric	stomach
2	chr11:62420800-62431600	Weak transcription	Small Intestine	intestine
3	chr11:62421200-62429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:62421200-62429600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:62421200-62429600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:62421200-62429600	Weak transcription	Left Ventricle	heart
7	chr11:62421200-62429600	Weak transcription	Lung	lung
8	chr11:62421200-62429600	Weak transcription	NHLF	lung
9	chr11:62421200-62429800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:62421200-62429800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:62421200-62429800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:62421200-62429800	Weak transcription	HMEC	breast
13	chr11:62421200-62430000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:62421200-62430000	Weak transcription	Spleen	Spleen
15	chr11:62421200-62430000	Weak transcription	HSMMtube	muscle
16	chr11:62421200-62430200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:62421200-62430200	Weak transcription	HSMM	muscle
18	chr11:62421200-62430600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:62421200-62430600	Weak transcription	Fetal Brain Male	brain
20	chr11:62421200-62431600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:62421200-62431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:62421200-62431600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:62421200-62431600	Weak transcription	NHDF-Ad	bronchial
24	chr11:62421200-62432000	Weak transcription	Aorta	Aorta
25	chr11:62421200-62432000	Weak transcription	Brain Substantia Nigra	brain
26	chr11:62421200-62432000	Weak transcription	Esophagus	oesophagus
27	chr11:62421200-62432000	Weak transcription	Ovary	ovary
28	chr11:62421200-62432000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:62421400-62429600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:62421400-62429600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:62421400-62429600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:62421400-62429600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:62421400-62429600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:62421400-62429600	Weak transcription	Brain Angular Gyrus	brain
35	chr11:62421400-62429600	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:62421400-62429600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:62421400-62429600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:62421400-62429600	Weak transcription	Thymus	Thymus
39	chr11:62421400-62429800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:62421400-62429800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:62421400-62429800	Weak transcription	Adipose Nuclei	Adipose
42	chr11:62421400-62429800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:62421400-62429800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr11:62421400-62430000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:62421400-62430000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:62421400-62430000	Weak transcription	Colonic Mucosa	Colon
47	chr11:62421400-62430000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:62421400-62430200	Weak transcription	Primary T cells from cord blood	blood
49	chr11:62421400-62430200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:62421400-62430200	Weak transcription	Muscle Satellite Cultured Cells	--

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