Variant report

Variant	rs9379962
Chromosome Location	chr6:27145311-27145312
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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27144640..27146653-chr6:27152847..27154919,2	K562	blood:
2	chr6:27144021..27146883-chr6:27258754..27261461,2	MCF-7	breast:
3	chr6:27144211..27146855-chr6:27719701..27721733,2	K562	blood:
4	chr6:27113708..27115397-chr6:27144002..27145832,2	MCF-7	breast:
5	chr6:27142668..27145341-chr6:27807841..27810817,2	K562	blood:
6	chr6:27144331..27145885-chr6:27758916..27760697,2	MCF-7	breast:
7	chr6:26193549..26195260-chr6:27144695..27146377,2	MCF-7	breast:
8	chr6:27144940..27148492-chr6:27773557..27776885,4	MCF-7	breast:
9	chr6:27135834..27138150-chr6:27143711..27145656,3	MCF-7	breast:
10	chr6:27143412..27146140-chr6:27152536..27156532,5	K562	blood:
11	chr6:27142864..27146588-chr6:27859215..27861126,3	K562	blood:
12	chr6:27143738..27145587-chr6:27441019..27442990,2	K562	blood:
13	chr6:27127283..27131812-chr6:27144311..27148515,7	MCF-7	breast:
14	chr6:27116861..27118975-chr6:27145251..27147249,2	MCF-7	breast:
15	chr6:27144310..27147077-chr6:27519122..27521076,2	K562	blood:
16	chr6:27143921..27146331-chr6:27500978..27503317,2	K562	blood:
17	chr6:27143840..27145814-chr6:27177507..27180295,2	K562	blood:
18	chr6:27115433..27117508-chr6:27144247..27145795,2	MCF-7	breast:
19	chr6:27145074..27147467-chr6:27777007..27779595,2	K562	blood:
20	chr6:27145253..27149186-chr6:27150759..27152469,4	K562	blood:
21	chr6:27144382..27146185-chr6:27797360..27798889,2	MCF-7	breast:
22	chr6:27124335..27127582-chr6:27143975..27147070,5	MCF-7	breast:
23	chr6:27097470..27099187-chr6:27144015..27145607,2	MCF-7	breast:
24	chr6:27144364..27147244-chr6:27219253..27220807,2	K562	blood:
25	chr6:27145218..27148337-chr6:27151646..27158450,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174572	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000217862	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2393918	0.81[ASN][1000 genomes]
rs4582379	0.81[ASN][1000 genomes]
rs6933999	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7745603	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs911186	0.81[EUR][1000 genomes]
rs9368489	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379961	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393790	0.88[AFR][1000 genomes]
rs9393791	0.89[AFR][1000 genomes]
rs9393792	0.83[ASN][1000 genomes]
rs9467989	0.84[AMR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9379962	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9379962	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs9379962	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27143800-27146200	Active TSS	Placenta	Placenta
2	chr6:27143800-27146800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:27143800-27146800	Active TSS	Fetal Lung	lung
4	chr6:27143800-27146800	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr6:27143800-27147000	Active TSS	HSMM	muscle
6	chr6:27143800-27147400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:27143800-27147400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:27143800-27147600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:27143800-27147600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:27144000-27146200	Active TSS	GM12878-XiMat	blood
11	chr6:27144000-27146600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:27144000-27146600	Active TSS	Left Ventricle	heart
13	chr6:27144000-27146600	Active TSS	Psoas Muscle	Psoas
14	chr6:27144000-27146800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr6:27144000-27146800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:27144000-27146800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:27144000-27146800	Active TSS	Ovary	ovary
18	chr6:27144000-27147000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:27144000-27147000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:27144000-27147000	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr6:27144000-27147000	Active TSS	NH-A	brain
22	chr6:27144000-27147200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr6:27144000-27147400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:27144000-27147600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:27144000-27147800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:27144200-27145400	Active TSS	Fetal Brain Female	brain
27	chr6:27144200-27145800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:27144200-27146000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr6:27144200-27146000	Active TSS	Dnd41	blood
30	chr6:27144200-27146000	Active TSS	HMEC	breast
31	chr6:27144200-27146000	Active TSS	K562	blood
32	chr6:27144200-27146200	Active TSS	Fetal Muscle Leg	muscle
33	chr6:27144200-27146600	Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr6:27144200-27146800	Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:27144200-27146800	Active TSS	NHDF-Ad	bronchial
36	chr6:27144200-27147000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:27144200-27147000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:27144200-27147000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:27144200-27147000	Active TSS	A549	lung
40	chr6:27144200-27147000	Active TSS	HSMMtube	muscle
41	chr6:27144200-27147000	Active TSS	Osteobl	bone
42	chr6:27144200-27147200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:27144200-27147200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:27144200-27147400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:27144200-27147600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:27144200-27147600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:27144400-27146000	Active TSS	Brain Hippocampus Middle	brain
48	chr6:27144400-27146200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:27144400-27146400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:27144400-27146400	Active TSS	Primary T killer memory cells from peripheral blood	blood

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