Variant report

Variant	rs7752448
Chromosome Location	chr6:28301099-28301100
allele	A/G
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28299865..28301376-chr6:28315526..28317433,2	MCF-7	breast:
2	chr6:28230115..28232269-chr6:28300762..28302458,2	MCF-7	breast:
3	chr6:27775597..27780846-chr6:28300467..28304976,7	K562	blood:
4	chr6:28282671..28284668-chr6:28300095..28302010,2	K562	blood:
5	chr6:28289244..28291635-chr6:28299932..28302110,2	MCF-7	breast:
6	chr6:28104111..28106206-chr6:28296771..28301344,4	K562	blood:
7	chr6:27774293..27778194-chr6:28301096..28304976,3	K562	blood:
8	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
9	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
10	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
11	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
12	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
13	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
14	chr6:28235909..28238714-chr6:28300665..28303049,3	MCF-7	breast:
15	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:
16	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
17	chr6:28273496..28275716-chr6:28299383..28301919,2	K562	blood:
18	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270326	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000238610	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1150722	1.00[JPT][hapmap]
rs1150723	1.00[JPT][hapmap]
rs1150725	1.00[JPT][hapmap]
rs1225600	1.00[JPT][hapmap]
rs13195291	0.90[CEU][hapmap]
rs13197633	0.90[CEU][hapmap]
rs13201308	0.90[CEU][hapmap]
rs13205211	0.90[CEU][hapmap]
rs13205911	0.90[CEU][hapmap]
rs13208096	0.82[CEU][hapmap]
rs13211507	0.90[CEU][hapmap]
rs13217619	0.90[CEU][hapmap]
rs1679723	1.00[JPT][hapmap]
rs1736892	1.00[JPT][hapmap]
rs1778510	1.00[JPT][hapmap]
rs2108924	1.00[JPT][hapmap]
rs2799076	1.00[JPT][hapmap]
rs2859375	1.00[JPT][hapmap]
rs3757180	1.00[JPT][hapmap]
rs3757183	1.00[JPT][hapmap]
rs6456812	1.00[JPT][hapmap]
rs6456817	1.00[JPT][hapmap]
rs6899512	1.00[JPT][hapmap]
rs6901001	1.00[JPT][hapmap]
rs6902583	1.00[JPT][hapmap]
rs6908459	1.00[JPT][hapmap]
rs6910120	1.00[JPT][hapmap]
rs6912921	1.00[JPT][hapmap]
rs6918043	1.00[JPT][hapmap]
rs6918631	1.00[JPT][hapmap]
rs6922161	1.00[JPT][hapmap]
rs6922302	1.00[JPT][hapmap]
rs6927023	1.00[JPT][hapmap]
rs6929449	1.00[JPT][hapmap]
rs6929559	1.00[JPT][hapmap]
rs6938371	1.00[JPT][hapmap]
rs7747772	0.81[ASN][1000 genomes]
rs7752608	0.90[EUR][1000 genomes]
rs7752721	1.00[JPT][hapmap]
rs7759855	1.00[JPT][hapmap]
rs7767897	1.00[JPT][hapmap]
rs9295769	1.00[JPT][hapmap]
rs9295770	1.00[JPT][hapmap]
rs9461450	1.00[JPT][hapmap]
rs9461457	1.00[JPT][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7752448	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs7752448	AL022393.7	cis	Muscle Skeletal	GTEx
rs7752448	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs7752448	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 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	chr6:28297200-28302200	Weak transcription	Brain Anterior Caudate	brain
20	chr6:28297200-28302200	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:28297200-28302400	Weak transcription	Adipose Nuclei	Adipose
22	chr6:28297200-28302400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:28297200-28302400	Weak transcription	Pancreas	Pancrea
24	chr6:28297200-28302400	Weak transcription	Right Ventricle	heart
25	chr6:28297200-28302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:28297200-28302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:28297200-28302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:28297200-28302800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:28297200-28302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:28297200-28302800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:28297200-28303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:28297400-28301400	Weak transcription	Lung	lung
33	chr6:28297400-28301800	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:28297400-28302200	Weak transcription	Fetal Brain Female	brain
35	chr6:28297400-28302400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:28297400-28302400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:28297400-28302400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:28297400-28302400	Weak transcription	Fetal Stomach	stomach
39	chr6:28297400-28302400	Weak transcription	Left Ventricle	heart
40	chr6:28297400-28302400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:28297400-28302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:28297400-28302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:28297400-28302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:28297400-28302800	Weak transcription	Fetal Intestine Large	intestine
45	chr6:28297400-28302800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:28297400-28302800	Weak transcription	Psoas Muscle	Psoas
47	chr6:28297400-28303400	Weak transcription	Ovary	ovary
48	chr6:28297400-28303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:28297600-28302200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:28297600-28302400	Weak transcription	Stomach Smooth Muscle	stomach

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