Variant report

Variant	rs16997761
Chromosome Location	chr21:40890920-40890921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40889963..40891050-chr21:41077484..41078432,7	MCF-7	breast:
2	chr21:40889992..40890995-chr21:41087409..41088601,6	MCF-7	breast:
3	chr21:40890342..40891575-chr21:41084640..41085747,7	MCF-7	breast:
4	chr21:40889961..40891928-chr21:40983982..40986182,2	MCF-7	breast:
5	chr21:40890554..40891390-chr21:41077384..41078170,2	MCF-7	breast:
6	chr21:40815529..40818322-chr21:40890161..40892801,2	MCF-7	breast:
7	chr21:40889185..40892036-chr21:40982501..40984839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184809	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000185437	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16997693	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16997709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16997763	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16997765	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16997766	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16997767	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17406216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17408203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7281891	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
2	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr21:40875800-40895200	Weak transcription	Brain Substantia Nigra	brain
4	chr21:40875800-40898600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr21:40876400-40894600	Weak transcription	Gastric	stomach
6	chr21:40876400-40897400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:40877000-40891000	Weak transcription	Pancreas	Pancrea
8	chr21:40877400-40899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr21:40880200-40899800	Weak transcription	Fetal Muscle Leg	muscle
10	chr21:40885600-40891000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr21:40887400-40895200	Weak transcription	Liver	Liver
12	chr21:40888000-40891400	Weak transcription	Left Ventricle	heart
13	chr21:40888000-40894800	Weak transcription	Aorta	Aorta
14	chr21:40888200-40891000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr21:40888200-40891400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr21:40888200-40895400	Weak transcription	Fetal Brain Male	brain
17	chr21:40888200-40907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr21:40888400-40895200	Weak transcription	Brain Anterior Caudate	brain
19	chr21:40890200-40891000	Enhancers	Brain Hippocampus Middle	brain
20	chr21:40890200-40891400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr21:40890200-40891600	Enhancers	Stomach Mucosa	stomach
22	chr21:40890200-40897400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:40890400-40891000	Enhancers	Fetal Kidney	kidney
24	chr21:40890400-40891200	Enhancers	Fetal Lung	lung
25	chr21:40890400-40891200	Enhancers	Fetal Muscle Trunk	muscle
26	chr21:40890400-40891400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:40890400-40892000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr21:40890600-40891000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr21:40890600-40891000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr21:40890600-40891000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr21:40890600-40891200	Enhancers	Duodenum Mucosa	Duodenum
32	chr21:40890600-40891600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr21:40890600-40891800	Enhancers	Fetal Heart	heart
34	chr21:40890800-40895200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr21:40890800-40895600	Weak transcription	Adipose Nuclei	Adipose

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