Variant report

Variant	rs6787566
Chromosome Location	chr3:53148595-53148596
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53130798..53133008-chr3:53147283..53149455,2	K562	blood:
2	chr3:53147634..53148660-chr3:53229191..53230888,15	K562	blood:
3	chr3:53147481..53152677-chr3:53161701..53165714,6	MCF-7	breast:
4	chr3:53147149..53149237-chr3:53228020..53230160,2	K562	blood:
5	chr3:53147705..53149046-chr3:53229640..53231117,6	MCF-7	breast:
6	chr3:53148133..53149133-chr3:53270420..53271199,2	K562	blood:
7	chr3:53147650..53148675-chr3:53229707..53230554,5	MCF-7	breast:
8	chr3:53148456..53152429-chr3:53152734..53156128,3	K562	blood:
9	chr3:53147149..53149280-chr3:53227312..53230160,3	K562	blood:
10	chr3:53148079..53148694-chr3:53228257..53229052,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3891626	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58624586	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6785768	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798092	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798309	0.94[YRI][hapmap]
rs72965386	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965387	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965388	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965401	1.00[AFR][1000 genomes];1.00[AMR][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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53107800-53151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:53119000-53154200	Weak transcription	Stomach Mucosa	stomach
3	chr3:53122800-53152200	Weak transcription	Small Intestine	intestine
4	chr3:53123200-53148600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr3:53124200-53151600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:53127000-53154200	Weak transcription	Right Atrium	heart
7	chr3:53133600-53152600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:53137400-53151400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53137400-53161600	Strong transcription	Fetal Intestine Small	intestine
10	chr3:53138000-53151000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:53138400-53151400	Weak transcription	Gastric	stomach
12	chr3:53139000-53151200	Weak transcription	Colonic Mucosa	Colon
13	chr3:53139200-53151200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:53139200-53151400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:53139200-53157400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:53139400-53151200	Weak transcription	Esophagus	oesophagus
17	chr3:53139400-53151400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:53139600-53151400	Weak transcription	Aorta	Aorta
19	chr3:53140800-53149200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:53142800-53161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:53143000-53149400	Strong transcription	GM12878-XiMat	blood
22	chr3:53143600-53150800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:53143600-53151000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:53143600-53151400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:53144000-53151000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:53144200-53148600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:53144200-53151000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:53144200-53151000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:53144200-53151000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:53144400-53149600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:53144400-53149600	Weak transcription	Fetal Kidney	kidney
32	chr3:53144600-53148800	Weak transcription	Pancreas	Pancrea
33	chr3:53144600-53149400	Weak transcription	Fetal Brain Female	brain
34	chr3:53145000-53151200	Weak transcription	Brain Germinal Matrix	brain
35	chr3:53145000-53161400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:53145400-53151400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:53145600-53148600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:53145800-53148600	Enhancers	Fetal Heart	heart
39	chr3:53145800-53148800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:53145800-53161200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr3:53146000-53148600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:53146000-53151000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:53146200-53149400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:53146200-53151000	Weak transcription	Hela-S3	cervix
45	chr3:53146200-53151200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:53146400-53148600	Weak transcription	Adipose Nuclei	Adipose
47	chr3:53146400-53149600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:53146400-53151000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:53146600-53151000	Weak transcription	Fetal Brain Male	brain
50	chr3:53147000-53148600	Enhancers	Left Ventricle	heart

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