Variant report

Variant	rs36162392
Chromosome Location	chr6:26569135-26569136
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:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26320916..26324695-chr6:26568559..26572226,5	K562	blood:
2	chr6:26171710..26174567-chr6:26566701..26569487,2	K562	blood:
3	chr6:26156493..26160609-chr6:26566713..26572551,10	K562	blood:
4	chr6:26525492..26528021-chr6:26567722..26570111,2	MCF-7	breast:
5	chr6:26536222..26540133-chr6:26565164..26569470,5	K562	blood:
6	chr6:26341264..26342451-chr6:26569043..26570054,3	K562	blood:
7	chr6:26209148..26211378-chr6:26567732..26569489,2	K562	blood:
8	chr6:26519454..26523332-chr6:26568814..26573401,9	K562	blood:
9	chr6:26568887..26570876-chr6:26573166..26576074,2	MCF-7	breast:
10	chr6:26568233..26570911-chr6:26596732..26598616,2	MCF-7	breast:
11	chr6:26568830..26570911-chr6:27113890..27117177,3	K562	blood:
12	chr6:26567325..26570025-chr6:26570280..26572074,2	MCF-7	breast:
13	chr6:26456882..26459678-chr6:26567698..26569705,2	K562	blood:
14	chr6:26569051..26574263-chr6:27058255..27061104,5	K562	blood:
15	chr6:26566413..26579648-chr6:26592370..26599609,38	K562	blood:
16	chr6:26318750..26323113-chr6:26568559..26574896,7	K562	blood:
17	chr6:26325742..26329401-chr6:26567650..26570455,4	K562	blood:
18	chr6:26568519..26570551-chr6:27058352..27060839,2	K562	blood:
19	chr6:26215231..26219129-chr6:26568240..26572057,4	K562	blood:
20	chr6:26537819..26539463-chr6:26567519..26569805,2	MCF-7	breast:
21	chr6:26553141..26555933-chr6:26567279..26569954,2	MCF-7	breast:
22	chr6:26331657..26333799-chr6:26567368..26569524,2	K562	blood:
23	chr6:26519760..26523332-chr6:26568841..26572559,5	K562	blood:
24	chr6:26329307..26333799-chr6:26568024..26573999,9	K562	blood:
25	chr6:26568882..26571175-chr6:26571456..26572979,2	K562	blood:
26	chr6:26519493..26522345-chr6:26567503..26569793,2	MCF-7	breast:
27	chr6:26537928..26538527-chr6:26569132..26569978,2	K562	blood:
28	chr6:26285527..26288388-chr6:26566429..26569428,2	K562	blood:
29	chr6:26471319..26475410-chr6:26567164..26571952,5	K562	blood:
30	chr6:26325462..26328933-chr6:26567431..26570210,5	K562	blood:
31	chr6:26530786..26533089-chr6:26568633..26571101,2	K562	blood:
32	chr6:26216366..26219129-chr6:26567690..26570174,4	K562	blood:
33	chr6:26219518..26221470-chr6:26568147..26570701,2	K562	blood:
34	chr6:26568033..26580216-chr6:26588796..26603066,49	K562	blood:
35	chr6:26504071..26506546-chr6:26568162..26569845,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000261353	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000112763	Chromatin interaction
ENSG00000220875	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13195509	0.85[EUR][1000 genomes]
rs13198716	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13212985	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13220261	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34104395	0.85[EUR][1000 genomes]
rs34148261	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34246779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34605993	0.83[EUR][1000 genomes]
rs34781270	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35076545	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35277236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400317	0.91[AMR][1000 genomes]
rs35433030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35555795	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35627490	0.85[EUR][1000 genomes]
rs35680819	0.85[EUR][1000 genomes]
rs36033628	0.85[EUR][1000 genomes]
rs3734542	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3734543	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3823158	0.85[EUR][1000 genomes]
rs45527431	0.91[AMR][1000 genomes]
rs66757203	0.85[EUR][1000 genomes]
rs66941101	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71557340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72844462	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs36162392	BTN3A2	cis	Stomach	GTEx
rs36162392	BTN3A2	cis	Heart Left Ventricle	GTEx
rs36162392	BTN3A2	cis	Muscle Skeletal	GTEx
rs36162392	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs36162392	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs36162392	BTN3A2	cis	Artery Tibial	GTEx
rs36162392	BTN3A2	cis	Nerve Tibial	GTEx
rs36162392	BTN3A2	cis	Artery Aorta	GTEx
rs36162392	BTN3A2	cis	Whole Blood	GTEx
rs36162392	BTN3A2	cis	Esophagus Muscularis	GTEx
rs36162392	BTN3A2	cis	Esophagus Mucosa	GTEx
rs36162392	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs36162392	BTN3A2	cis	lung	GTEx
rs36162392	BTN3A2	cis	Thyroid	GTEx
rs36162392	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26568000-26569200	Active TSS	Hela-S3	cervix
2	chr6:26568000-26569800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:26568000-26569800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:26568000-26569800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:26568000-26569800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:26568000-26570000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:26568000-26570000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:26568000-26570200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:26568200-26569200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr6:26568200-26569200	Active TSS	Osteobl	bone
11	chr6:26568200-26569400	Active TSS	Primary hematopoietic stem cells	blood
12	chr6:26568200-26569400	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr6:26568200-26569400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr6:26568200-26569400	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:26568200-26569400	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:26568200-26569400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:26568200-26569400	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr6:26568200-26569400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:26568200-26569400	Active TSS	Brain Germinal Matrix	brain
20	chr6:26568200-26569400	Active TSS	Fetal Brain Female	brain
21	chr6:26568200-26569400	Active TSS	Fetal Muscle Trunk	muscle
22	chr6:26568200-26569400	Active TSS	Stomach Smooth Muscle	stomach
23	chr6:26568200-26569400	Active TSS	HepG2	liver
24	chr6:26568200-26569400	Active TSS	HUVEC	blood vessel
25	chr6:26568200-26569600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:26568200-26569600	Active TSS	Primary T cells from cord blood	blood
27	chr6:26568200-26569600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:26568200-26569600	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr6:26568200-26569600	Active TSS	Fetal Kidney	kidney
30	chr6:26568200-26569600	Active TSS	Rectal Smooth Muscle	rectum
31	chr6:26568200-26569600	Active TSS	GM12878-XiMat	blood
32	chr6:26568200-26569800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:26568200-26569800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:26568200-26569800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:26568200-26569800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:26568200-26569800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:26568200-26569800	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:26568200-26569800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:26568200-26569800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:26568200-26569800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr6:26568200-26569800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:26568200-26569800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:26568200-26569800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:26568200-26569800	Active TSS	Brain Angular Gyrus	brain
45	chr6:26568200-26569800	Active TSS	Brain Anterior Caudate	brain
46	chr6:26568200-26569800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:26568200-26569800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:26568200-26569800	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:26568200-26569800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:26568200-26569800	Active TSS	Right Atrium	heart

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