Variant report

Variant	rs62256003
Chromosome Location	chr3:53283952-53283953
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53282491..53286758-chr3:53287434..53291520,6	K562	blood:
2	chr3:53282491..53286758-chr3:53287434..53291487,8	K562	blood:
3	chr3:53276909..53279074-chr3:53282847..53285321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10433617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433618	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108506	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030934	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17234771	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235667	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41275543	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59145995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255993	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255994	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255999	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256000	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256009	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256043	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256049	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256050	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256053	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62256965	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256966	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256968	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256969	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257004	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62257007	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62257009	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62257011	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62257013	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62257024	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6780100	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73080266	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73082274	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7622159	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830594	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830895	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846315	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9850440	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864057	0.85[EUR][1000 genomes];0.90[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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53272800-53286600	Weak transcription	Fetal Brain Male	brain
2	chr3:53272800-53288000	Weak transcription	Fetal Kidney	kidney
3	chr3:53276200-53287400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:53276400-53284000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:53276600-53285200	Weak transcription	HSMM	muscle
6	chr3:53277200-53285600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:53277600-53286200	Weak transcription	Fetal Intestine Large	intestine
8	chr3:53277800-53284800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:53278400-53284200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:53278400-53284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:53278600-53284800	Weak transcription	NH-A	brain
12	chr3:53278600-53285400	Weak transcription	Ovary	ovary
13	chr3:53278600-53285600	Weak transcription	Aorta	Aorta
14	chr3:53278600-53288000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:53278800-53284200	Weak transcription	Osteobl	bone
16	chr3:53278800-53284400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:53278800-53286000	Weak transcription	Small Intestine	intestine
18	chr3:53278800-53287800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:53278800-53288200	Weak transcription	Psoas Muscle	Psoas
20	chr3:53279000-53285000	Weak transcription	Stomach Mucosa	stomach
21	chr3:53279600-53284000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:53279600-53284000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:53280200-53285000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:53280200-53288000	Weak transcription	Fetal Stomach	stomach
25	chr3:53280400-53288000	Weak transcription	Fetal Brain Female	brain
26	chr3:53280600-53284000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:53280600-53284200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:53280600-53285200	Weak transcription	NHDF-Ad	bronchial
29	chr3:53280600-53288000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:53281400-53288000	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:53281600-53285200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:53281600-53286200	Enhancers	Fetal Thymus	thymus
33	chr3:53281600-53288000	Enhancers	Thymus	Thymus
34	chr3:53281600-53288400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr3:53281800-53284200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:53281800-53285000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr3:53281800-53286800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:53281800-53287800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:53281800-53288000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:53281800-53288600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:53282000-53286400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:53282000-53288000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr3:53282200-53284000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:53282200-53285400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:53282200-53287200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:53282400-53284200	Weak transcription	HMEC	breast
47	chr3:53282400-53288000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr3:53282600-53285000	Weak transcription	Esophagus	oesophagus
49	chr3:53282600-53286800	Weak transcription	Colonic Mucosa	Colon
50	chr3:53282600-53289600	Flanking Active TSS	Primary B cells from cord blood	blood

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