Variant report

Variant	rs12490555
Chromosome Location	chr3:53228836-53228837
allele	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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53147149..53149237-chr3:53228020..53230160,2	K562	blood:
2	chr3:53147149..53149280-chr3:53227312..53230160,3	K562	blood:
3	chr3:53162914..53166776-chr3:53227642..53231042,4	MCF-7	breast:
4	chr3:53154170..53157066-chr3:53227293..53230182,2	MCF-7	breast:
5	chr3:53197949..53201671-chr3:53227603..53230780,3	MCF-7	breast:
6	chr3:53155385..53158103-chr3:53228552..53231241,3	K562	blood:
7	chr3:53149564..53151177-chr3:53228526..53230343,2	K562	blood:
8	chr3:53148079..53148694-chr3:53228257..53229052,2	MCF-7	breast:
9	chr3:53192673..53196741-chr3:53226099..53230036,6	MCF-7	breast:
10	chr3:53228679..53231516-chr3:53231872..53234028,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163932	Chromatin interaction
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12490645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230494	0.82[ASN][1000 genomes]
rs2306572	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2306574	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773722	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs45596236	0.82[ASN][1000 genomes]
rs57742023	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62254320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:53202800-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:53203600-53229800	Weak transcription	A549	lung
4	chr3:53205600-53229800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:53210000-53229000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:53214200-53229600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:53214400-53229600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:53214800-53229600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:53214800-53229800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:53215000-53229800	Weak transcription	Fetal Brain Female	brain
11	chr3:53216000-53229800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:53216200-53229800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:53217800-53229600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:53217800-53229800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:53219400-53229800	Weak transcription	K562	blood
16	chr3:53220000-53230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:53223200-53229200	Strong transcription	Fetal Intestine Small	intestine
18	chr3:53223800-53229000	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr3:53224000-53229800	Weak transcription	Brain Germinal Matrix	brain
20	chr3:53224400-53229200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:53224400-53229800	Weak transcription	NHDF-Ad	bronchial
22	chr3:53224600-53230800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:53224800-53229800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:53225000-53229600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:53225000-53229600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:53225000-53229800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:53225200-53230200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:53225400-53229600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr3:53225800-53229600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:53226000-53230000	Genic enhancers	Spleen	Spleen
31	chr3:53226200-53229800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:53226200-53229800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:53226200-53230600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:53226400-53229600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:53226400-53229800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:53226600-53229600	Weak transcription	Primary B cells from cord blood	blood
37	chr3:53226800-53229200	Genic enhancers	Fetal Stomach	stomach
38	chr3:53226800-53229600	Enhancers	Fetal Muscle Leg	muscle
39	chr3:53226800-53229800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:53226800-53231000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr3:53227000-53229000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:53227000-53229000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:53227000-53229200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:53227200-53229000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:53227200-53229600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:53227400-53229000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr3:53227400-53229000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:53227400-53229000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:53227400-53229000	Enhancers	Right Atrium	heart
50	chr3:53227400-53229200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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