Variant report

Variant	rs28613540
Chromosome Location	chr3:69836610-69836611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69826342..69828033-chr3:69835897..69837657,2	MCF-7	breast:
2	chr3:69820056..69823613-chr3:69833464..69836716,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11128143	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367369	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17043851	0.80[ASN][1000 genomes]
rs2116000	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28378222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4605553	0.80[ASN][1000 genomes]
rs4855448	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55921103	0.86[ASN][1000 genomes]
rs55947901	0.82[ASN][1000 genomes]
rs57537586	0.85[ASN][1000 genomes]
rs58244283	0.82[ASN][1000 genomes]
rs62250976	0.86[ASN][1000 genomes]
rs62250977	0.87[ASN][1000 genomes]
rs6762369	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6785461	0.88[ASN][1000 genomes]
rs6786207	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6786226	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7648607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834743	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][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	esv3507784	chr3:69802539-69959607	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3507785	chr3:69802539-69959607	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1009045	chr3:69821621-69875782	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69824000-69837000	Weak transcription	Lung	lung
2	chr3:69827400-69839200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr3:69833200-69837200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:69833200-69837200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:69833200-69837200	Enhancers	NHLF	lung
6	chr3:69833200-69838000	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:69833400-69837200	Enhancers	NHDF-Ad	bronchial
8	chr3:69833600-69837200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:69833800-69836800	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:69833800-69837200	Enhancers	Fetal Lung	lung
11	chr3:69833800-69837200	Enhancers	Hela-S3	cervix
12	chr3:69833800-69837200	Enhancers	NHEK	skin
13	chr3:69834000-69837200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:69834000-69837200	Enhancers	Adipose Nuclei	Adipose
15	chr3:69834200-69837200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:69834200-69837200	Enhancers	HSMM	muscle
17	chr3:69834600-69839800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:69834600-69840400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:69834800-69837200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:69834800-69837200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:69834800-69837200	Enhancers	K562	blood
22	chr3:69834800-69839800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:69834800-69840200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:69835000-69837000	Enhancers	Colon Smooth Muscle	Colon
25	chr3:69835000-69840000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:69835000-69840400	Weak transcription	Fetal Thymus	thymus
27	chr3:69835200-69839800	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:69835200-69840200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:69835400-69840600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:69835600-69840800	Weak transcription	Left Ventricle	heart
31	chr3:69835600-69840800	Weak transcription	Right Ventricle	heart
32	chr3:69836000-69836800	Flanking Active TSS	HSMMtube	muscle
33	chr3:69836000-69837200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:69836000-69837200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:69836000-69837200	Enhancers	HUVEC	blood vessel
36	chr3:69836000-69837200	Enhancers	Osteobl	bone
37	chr3:69836200-69836800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:69836200-69837200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:69836200-69837200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:69836200-69837200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:69836200-69837200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:69836200-69837200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:69836200-69837200	Enhancers	Brain Substantia Nigra	brain
44	chr3:69836200-69837200	Enhancers	HMEC	breast
45	chr3:69836400-69837000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:69836400-69837000	Flanking Active TSS	A549	lung
47	chr3:69836400-69837200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:69836400-69837200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr3:69836400-69837200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:69836400-69837200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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