Variant report

Variant	rs56401801
Chromosome Location	chr6:27301512-27301513
allele	A/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27218055..27220276-chr6:27300325..27303096,3	K562	blood:
2	chr6:27298779..27303006-chr6:27440534..27442735,4	K562	blood:
3	chr6:27299766..27302375-chr6:27444830..27446395,2	K562	blood:
4	chr6:27258451..27260109-chr6:27301059..27302632,2	K562	blood:
5	chr6:27298898..27303175-chr6:27340830..27343404,5	K562	blood:
6	chr6:27287824..27293332-chr6:27295713..27302247,8	K562	blood:
7	chr6:27291413..27293040-chr6:27299829..27302713,2	MCF-7	breast:
8	chr6:27264150..27266831-chr6:27300629..27302449,2	K562	blood:
9	chr6:27300837..27303680-chr6:27307517..27309958,2	K562	blood:
10	chr6:27277495..27280431-chr6:27299498..27302391,2	K562	blood:
11	chr6:27263999..27267440-chr6:27299677..27302604,5	K562	blood:
12	chr6:27276791..27280576-chr6:27298923..27302888,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000158553	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13191227	0.89[EUR][1000 genomes]
rs13191474	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13195040	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13196692	0.89[EUR][1000 genomes]
rs13207082	0.89[EUR][1000 genomes]
rs13207689	0.90[EUR][1000 genomes]
rs13212562	0.91[EUR][1000 genomes]
rs13218537	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360634	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34071253	0.87[EUR][1000 genomes]
rs34196306	0.81[EUR][1000 genomes]
rs34332556	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953377	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120058	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35716472	0.87[EUR][1000 genomes]
rs35984974	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269265	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56114371	0.89[EUR][1000 genomes]
rs66841633	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67859638	0.90[EUR][1000 genomes]
rs71537559	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839445	0.89[EUR][1000 genomes]
rs72839477	0.94[EUR][1000 genomes]
rs9468033	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2761047	chr6:27296775-27303927	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs56401801	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs56401801	BTN3A2	cis	Muscle Skeletal	GTEx
rs56401801	BTN3A2	cis	Nerve Tibial	GTEx
rs56401801	BTN3A2	cis	Esophagus Muscularis	GTEx
rs56401801	BTN3A2	cis	Whole Blood	GTEx
rs56401801	BTN3A2	cis	Artery Aorta	GTEx
rs56401801	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs56401801	BTN3A2	cis	Esophagus Mucosa	GTEx
rs56401801	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs56401801	BTN3A2	cis	Artery Tibial	GTEx
rs56401801	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs56401801	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs56401801	BTN3A2	cis	Thyroid	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27300200-27303200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27300200-27303400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27300400-27301600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:27300400-27301600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:27300400-27301600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:27300400-27301800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:27300400-27301800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:27300400-27302000	Active TSS	GM12878-XiMat	blood
9	chr6:27300400-27302400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:27300400-27303200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:27300400-27303200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:27300400-27303400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:27300400-27303600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:27300600-27301600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:27300600-27301600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:27300600-27301600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:27300600-27301600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:27300600-27301600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:27300600-27301600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:27300600-27301600	Active TSS	NHLF	lung
21	chr6:27300600-27301800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:27300600-27302000	Active TSS	K562	blood
23	chr6:27300600-27302200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:27300600-27302200	Active TSS	HMEC	breast
25	chr6:27300800-27301600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:27300800-27301600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:27300800-27301600	Active TSS	Brain Anterior Caudate	brain
28	chr6:27300800-27301600	Active TSS	Brain Hippocampus Middle	brain
29	chr6:27300800-27301600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr6:27300800-27301600	Active TSS	Osteobl	bone
31	chr6:27300800-27301800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:27300800-27301800	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr6:27300800-27301800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:27300800-27302000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:27300800-27302000	Active TSS	A549	lung
36	chr6:27300800-27302000	Active TSS	NHEK	skin
37	chr6:27301000-27301600	Active TSS	HepG2	liver
38	chr6:27301200-27301600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:27301400-27301600	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
40	chr6:27301400-27301600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr6:27301400-27301600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:27301400-27301800	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:27301400-27301800	Active TSS	HUVEC	blood vessel
44	chr6:27301400-27321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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