Variant report

Variant	rs60502621
Chromosome Location	chr3:24499560-24499561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24497472..24501858-chr3:24535149..24538807,5	MCF-7	breast:
2	chr3:24496916..24499830-chr3:24502465..24505950,4	K562	blood:
3	chr3:24498226..24500765-chr3:24535657..24537562,2	MCF-7	breast:
4	chr3:24497480..24499832-chr3:24520905..24522991,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKIRAS1-2	chr3:24499468-24500925	ENSG00000224822.1

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12488078	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490491	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1865711	0.90[EUR][1000 genomes]
rs56783261	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58274299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58388581	0.90[EUR][1000 genomes]
rs58932894	0.90[EUR][1000 genomes]
rs61063562	0.90[EUR][1000 genomes]
rs6789815	0.91[ASN][1000 genomes]
rs73823308	0.95[EUR][1000 genomes]
rs73823340	0.95[EUR][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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24491200-24502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:24492400-24502200	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:24493200-24501800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:24493600-24502000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:24493600-24504200	Weak transcription	Left Ventricle	heart
6	chr3:24495400-24504800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:24497400-24502000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:24497600-24502400	Weak transcription	Liver	Liver
9	chr3:24498600-24499600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:24498600-24499800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:24498600-24499800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:24498600-24500200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:24498800-24499800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr3:24498800-24499800	Enhancers	Psoas Muscle	Psoas
15	chr3:24499000-24502200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:24499000-24502200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:24499200-24499600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:24499200-24499600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr3:24499200-24499800	Enhancers	Fetal Intestine Large	intestine
20	chr3:24499400-24499600	Enhancers	Aorta	Aorta
21	chr3:24499400-24500000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:24499400-24502200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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