Variant report

Variant	rs72854524
Chromosome Location	chr6:28300315-28300316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28299865..28301376-chr6:28315526..28317433,2	MCF-7	breast:
2	chr6:28282671..28284668-chr6:28300095..28302010,2	K562	blood:
3	chr6:28289244..28291635-chr6:28299932..28302110,2	MCF-7	breast:
4	chr6:28104111..28106206-chr6:28296771..28301344,4	K562	blood:
5	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
6	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
7	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
8	chr6:28265276..28267226-chr6:28297300..28300691,3	MCF-7	breast:
9	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
10	chr6:28271589..28273882-chr6:28298871..28300680,2	K562	blood:
11	chr6:28273496..28275716-chr6:28299383..28301919,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261839	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2079705	1.00[AMR][1000 genomes]
rs41269289	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41270579	1.00[AMR][1000 genomes]
rs4540253	1.00[AMR][1000 genomes]
rs72844212	1.00[AMR][1000 genomes]
rs72850297	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72854503	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72854515	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72854522	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72854525	0.94[EUR][1000 genomes]
rs72854527	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72854531	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72854533	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72854535	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72854536	0.87[EUR][1000 genomes]
rs72854542	1.00[AMR][1000 genomes]
rs72854546	1.00[AMR][1000 genomes]
rs72854553	1.00[AMR][1000 genomes]
rs72854556	1.00[AMR][1000 genomes]
rs7752415	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28294800-28302000	Weak transcription	HepG2	liver
2	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:28295400-28301400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
5	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
8	chr6:28295600-28302000	Weak transcription	Fetal Heart	heart
9	chr6:28295600-28302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:28295600-28302200	Weak transcription	Hela-S3	cervix
11	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
12	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
13	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
15	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28297000-28302000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28297000-28302800	Weak transcription	Colonic Mucosa	Colon
18	chr6:28297000-28303400	Weak transcription	Gastric	stomach
19	chr6:28297200-28300400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:28297200-28302200	Weak transcription	Brain Anterior Caudate	brain
21	chr6:28297200-28302200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28297200-28302400	Weak transcription	Adipose Nuclei	Adipose
23	chr6:28297200-28302400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:28297200-28302400	Weak transcription	Pancreas	Pancrea
25	chr6:28297200-28302400	Weak transcription	Right Ventricle	heart
26	chr6:28297200-28302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:28297200-28302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:28297200-28302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:28297200-28302800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:28297200-28302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:28297200-28302800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:28297200-28303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:28297400-28301400	Weak transcription	Lung	lung
34	chr6:28297400-28301800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:28297400-28302200	Weak transcription	Fetal Brain Female	brain
36	chr6:28297400-28302400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:28297400-28302400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:28297400-28302400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:28297400-28302400	Weak transcription	Fetal Stomach	stomach
40	chr6:28297400-28302400	Weak transcription	Left Ventricle	heart
41	chr6:28297400-28302400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:28297400-28302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:28297400-28302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:28297400-28302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:28297400-28302800	Weak transcription	Fetal Intestine Large	intestine
46	chr6:28297400-28302800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:28297400-28302800	Weak transcription	Psoas Muscle	Psoas
48	chr6:28297400-28303400	Weak transcription	Ovary	ovary
49	chr6:28297400-28303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:28297600-28302200	Weak transcription	Brain Inferior Temporal Lobe	brain

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