Variant report

Variant	rs56220620
Chromosome Location	chr3:143566870-143566871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1394398	1.00[ASN][1000 genomes]
rs1504603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1504604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1995529	1.00[ASN][1000 genomes]
rs1995530	1.00[ASN][1000 genomes]
rs2011297	0.93[ASN][1000 genomes]
rs2011303	1.00[ASN][1000 genomes]
rs2361205	0.85[ASN][1000 genomes]
rs2885195	1.00[ASN][1000 genomes]
rs4499594	1.00[ASN][1000 genomes]
rs56407400	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57718888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58887384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58921154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59306133	1.00[ASN][1000 genomes]
rs60249173	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60523819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60550983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6768702	0.93[ASN][1000 genomes]
rs6780027	0.93[ASN][1000 genomes]
rs6794907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869037	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869039	0.85[ASN][1000 genomes]
rs73869041	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869049	1.00[ASN][1000 genomes]
rs73869050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871826	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871827	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73871828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7434217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7613146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7637640	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9824974	1.00[ASN][1000 genomes]
rs9836851	0.93[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143563200-143567600	Active TSS	GM12878-XiMat	blood
2	chr3:143565200-143567400	Active TSS	Placenta	Placenta
3	chr3:143565200-143567400	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr3:143565400-143567600	Active TSS	Brain Hippocampus Middle	brain
5	chr3:143565400-143567600	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:143565400-143567600	Active TSS	NHDF-Ad	bronchial
7	chr3:143565800-143567000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr3:143565800-143567400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:143565800-143567400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:143565800-143567400	Active TSS	Liver	Liver
11	chr3:143565800-143567400	Active TSS	NHLF	lung
12	chr3:143565800-143567600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:143565800-143567600	Active TSS	Primary T cells fromperipheralblood	blood
14	chr3:143565800-143567600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:143565800-143567600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:143565800-143567600	Active TSS	Duodenum Mucosa	Duodenum
17	chr3:143565800-143567600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:143565800-143567600	Active TSS	Fetal Stomach	stomach
19	chr3:143565800-143567600	Active TSS	Psoas Muscle	Psoas
20	chr3:143565800-143567600	Active TSS	Right Atrium	heart
21	chr3:143565800-143567800	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr3:143565800-143569200	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr3:143566000-143567200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:143566000-143567200	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr3:143566000-143567400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:143566000-143567400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:143566000-143567400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:143566000-143567400	Active TSS	Fetal Intestine Small	intestine
29	chr3:143566000-143567400	Active TSS	Fetal Thymus	thymus
30	chr3:143566000-143567400	Active TSS	Thymus	Thymus
31	chr3:143566000-143567600	Active TSS	Brain Substantia Nigra	brain
32	chr3:143566000-143567600	Active TSS	Colon Smooth Muscle	Colon
33	chr3:143566000-143567600	Active TSS	Fetal Muscle Leg	muscle
34	chr3:143566000-143567800	Flanking Active TSS	Dnd41	blood
35	chr3:143566000-143568200	Active TSS	Brain Anterior Caudate	brain
36	chr3:143566000-143568400	Active TSS	Ovary	ovary
37	chr3:143566200-143567400	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:143566200-143567400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:143566200-143567400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:143566200-143567400	Active TSS	Adipose Nuclei	Adipose
41	chr3:143566200-143567400	Active TSS	Brain Germinal Matrix	brain
42	chr3:143566200-143567400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr3:143566200-143567400	Active TSS	Fetal Intestine Large	intestine
44	chr3:143566200-143567400	Active TSS	Fetal Muscle Trunk	muscle
45	chr3:143566200-143567400	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:143566200-143567600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:143566200-143567600	Active TSS	Brain Angular Gyrus	brain
48	chr3:143566200-143567600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:143566200-143567600	Active TSS	Fetal Lung	lung
50	chr3:143566200-143567800	Active TSS	Fetal Kidney	kidney

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