Variant report

Variant	rs59090383
Chromosome Location	chr3:69161280-69161281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69134058..69135768-chr3:69160353..69162971,2	MCF-7	breast:
2	chr3:69133988..69135685-chr3:69160531..69162291,2	K562	blood:
3	chr3:69129750..69131406-chr3:69159506..69161927,2	MCF-7	breast:
4	chr3:69153444..69155316-chr3:69160247..69161792,2	MCF-7	breast:
5	chr3:69157140..69159067-chr3:69160070..69162293,2	K562	blood:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1051901	1.00[EUR][1000 genomes]
rs1131960	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054346	1.00[EUR][1000 genomes]
rs17005366	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772980	1.00[EUR][1000 genomes]
rs3772983	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796214	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821564	1.00[EUR][1000 genomes]
rs56152276	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56194306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56280964	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57159802	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58277851	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60474520	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61086164	0.98[ASN][1000 genomes]
rs72924853	1.00[EUR][1000 genomes]
rs72924854	1.00[EUR][1000 genomes]
rs73835715	0.94[ASN][1000 genomes]
rs73835716	0.98[ASN][1000 genomes]
rs73835722	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835726	1.00[EUR][1000 genomes]
rs73835727	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835728	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73835729	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617775	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621394	1.00[EUR][1000 genomes]
rs7621929	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv2762334	chr3:69157085-69173375	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69153800-69162400	Weak transcription	HMEC	breast
2	chr3:69153800-69165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:69153800-69168000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:69154000-69162000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:69154000-69162200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:69154000-69163200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:69154000-69164800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:69154000-69164800	Weak transcription	Right Atrium	heart
9	chr3:69154000-69164800	Weak transcription	NHEK	skin
10	chr3:69154000-69165000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:69154000-69165800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:69154000-69167800	Weak transcription	Pancreas	Pancrea
13	chr3:69154000-69170200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:69154200-69162000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:69154400-69163000	Weak transcription	Fetal Lung	lung
16	chr3:69154400-69166000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:69155400-69164800	Weak transcription	NH-A	brain
18	chr3:69155400-69165800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:69155600-69162400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:69155600-69164800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:69155800-69162200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:69155800-69162400	Weak transcription	HSMM	muscle
23	chr3:69155800-69162400	Weak transcription	NHLF	lung
24	chr3:69155800-69162600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:69155800-69165400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:69155800-69166200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:69155800-69170200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:69156400-69162200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:69156400-69162800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:69158400-69167200	Weak transcription	Brain Anterior Caudate	brain
31	chr3:69158600-69162400	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:69158600-69162800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:69158600-69163200	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:69159400-69161600	Weak transcription	HSMMtube	muscle
35	chr3:69160200-69163800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:69160200-69163800	Enhancers	Osteobl	bone
37	chr3:69160400-69165800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:69160600-69161400	Weak transcription	Right Ventricle	heart
39	chr3:69160600-69162600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:69160600-69162800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:69160600-69163200	Weak transcription	Left Ventricle	heart
42	chr3:69160600-69172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:69161000-69161400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:69161200-69162000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
45	chr3:69161200-69163600	Enhancers	NHDF-Ad	bronchial
46	chr3:69161200-69164000	Enhancers	Psoas Muscle	Psoas
47	chr3:69161200-69164800	Enhancers	Fetal Heart	heart

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