Variant report

Variant	rs72839477
Chromosome Location	chr6:27327000-27327001
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:1)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27177161..27179137-chr6:27326485..27328754,2	K562	blood:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POM121L2-2	chr6:27325602-27328000	NONHSAT108367
2	lnc-POM121L2-2	chr6:27325602-27328000	NONHSAT108368
3	lnc-POM121L2-2	chr6:27325604-27328000	NONHSAT108369
4	lnc-POM121L2-2	chr6:27325607-27328000	NONHSAT108370
5	lnc-POM121L2-2	chr6:27325619-27328000	NONHSAT108373
6	lnc-POM121L2-2	chr6:27325656-27328000	NONHSAT108374

No data

Variant related genes	Relation type
ENSG00000174572	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13191227	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13191474	0.87[EUR][1000 genomes]
rs13195040	0.87[EUR][1000 genomes]
rs13195636	0.81[EUR][1000 genomes]
rs13196692	0.94[EUR][1000 genomes]
rs13207082	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13207689	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13209332	0.81[EUR][1000 genomes]
rs13212562	0.86[EUR][1000 genomes]
rs13218537	0.94[EUR][1000 genomes]
rs28360634	1.00[EUR][1000 genomes]
rs34071253	0.92[EUR][1000 genomes]
rs34196306	0.87[EUR][1000 genomes]
rs34332556	0.94[EUR][1000 genomes]
rs34573979	0.85[EUR][1000 genomes]
rs34953377	0.94[EUR][1000 genomes]
rs34965299	0.81[EUR][1000 genomes]
rs35120058	0.94[EUR][1000 genomes]
rs35716472	0.92[EUR][1000 genomes]
rs35848276	0.81[EUR][1000 genomes]
rs35984974	0.92[EUR][1000 genomes]
rs41269265	0.87[EUR][1000 genomes]
rs56114371	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56401801	0.94[EUR][1000 genomes]
rs58616630	0.85[EUR][1000 genomes]
rs66785117	0.81[EUR][1000 genomes]
rs66841633	0.94[EUR][1000 genomes]
rs67859638	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71537559	0.96[EUR][1000 genomes]
rs72839445	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs72839477	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs72839477	BTN3A2	cis	Thyroid	GTEx
rs72839477	BTN3A2	cis	Esophagus Mucosa	GTEx
rs72839477	BTN3A2	cis	Esophagus Muscularis	GTEx
rs72839477	BTN3A2	cis	Muscle Skeletal	GTEx
rs72839477	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs72839477	BTN3A2	cis	Whole Blood	GTEx
rs72839477	BTN3A2	cis	lung	GTEx
rs72839477	BTN3A2	cis	Heart Left Ventricle	GTEx
rs72839477	BTN3A2	cis	Artery Tibial	GTEx
rs72839477	BTN3A2	cis	Nerve Tibial	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27316800-27335400	Weak transcription	Pancreas	Pancrea
2	chr6:27323600-27327000	Weak transcription	Brain Angular Gyrus	brain
3	chr6:27325600-27328200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
4	chr6:27325800-27336200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:27326000-27327000	Weak transcription	Fetal Brain Male	brain
6	chr6:27326000-27327600	ZNF genes & repeats	Psoas Muscle	Psoas
7	chr6:27326000-27328000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
8	chr6:27326000-27331200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr6:27326000-27335600	Weak transcription	Brain Germinal Matrix	brain
10	chr6:27326200-27327000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
11	chr6:27326200-27328200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
12	chr6:27326200-27328200	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr6:27326200-27331000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:27326400-27327200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
15	chr6:27326400-27327400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
16	chr6:27326400-27327400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr6:27326400-27327600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
18	chr6:27326400-27327600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:27326400-27327600	ZNF genes & repeats	Left Ventricle	heart
20	chr6:27326400-27328200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr6:27326400-27328200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
22	chr6:27326400-27328400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
23	chr6:27326400-27329600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr6:27326400-27331800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:27326600-27327200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
26	chr6:27326600-27327400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:27326600-27327400	ZNF genes & repeats	Brain Anterior Caudate	brain
28	chr6:27326600-27327400	ZNF genes & repeats	Fetal Kidney	kidney
29	chr6:27326600-27327600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr6:27326600-27327600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
31	chr6:27326600-27327800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
32	chr6:27326600-27328000	ZNF genes & repeats	Ovary	ovary
33	chr6:27326600-27328200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr6:27326600-27328200	ZNF genes & repeats	Right Ventricle	heart
35	chr6:27326600-27328800	ZNF genes & repeats	Fetal Lung	lung
36	chr6:27326600-27329400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr6:27326800-27327200	ZNF genes & repeats	Fetal Heart	heart
38	chr6:27326800-27327400	ZNF genes & repeats	Aorta	Aorta
39	chr6:27326800-27327400	ZNF genes & repeats	Gastric	stomach
40	chr6:27326800-27327400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
41	chr6:27326800-27327600	ZNF genes & repeats	Liver	Liver
42	chr6:27326800-27327600	ZNF genes & repeats	Brain Substantia Nigra	brain
43	chr6:27326800-27328200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
44	chr6:27326800-27328200	ZNF genes & repeats	Brain Hippocampus Middle	brain
45	chr6:27326800-27328400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:27326800-27330800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr6:27326800-27331200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:27326800-27342000	Weak transcription	Colonic Mucosa	Colon
49	chr6:27327000-27327400	ZNF genes & repeats	Fetal Brain Male	brain
50	chr6:27327000-27327600	Strong transcription	Brain Angular Gyrus	brain

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