Variant report

Variant	rs67457459
Chromosome Location	chr6:27198343-27198344
allele	G/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:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27100701..27102362-chr6:27197500..27199646,2	K562	blood:
2	chr6:27192498..27195500-chr6:27198039..27200217,4	K562	blood:
3	chr6:27196971..27199808-chr6:27204338..27205850,2	MCF-7	breast:
4	chr6:27192383..27194653-chr6:27197243..27199028,2	MCF-7	breast:
5	chr6:27197426..27201736-chr6:27203200..27207154,7	K562	blood:
6	chr6:27198164..27199852-chr6:27213905..27216503,2	K562	blood:
7	chr6:27114077..27118449-chr6:27196059..27200185,5	K562	blood:
8	chr6:27195411..27200167-chr6:27200252..27206108,10	K562	blood:
9	chr6:27196755..27199547-chr6:27440103..27442239,2	K562	blood:
10	chr6:27197041..27202373-chr6:27261458..27267425,7	K562	blood:
11	chr6:27197164..27198769-chr6:27245728..27247415,2	K562	blood:
12	chr6:27129888..27131649-chr6:27195657..27199036,3	K562	blood:
13	chr6:27198091..27199769-chr6:27253992..27255811,2	K562	blood:
14	chr6:27198224..27199922-chr6:27229756..27232749,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS16-1	chr6:27198177-27198434	NONHSAT108350

No data

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13212921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13219354	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34817112	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35909544	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4452638	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56862318	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs67457459	BTN3A2	cis	lung	GTEx
rs67457459	BTN3A2	cis	Whole Blood	GTEx
rs67457459	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs67457459	BTN3A2	cis	Esophagus Muscularis	GTEx
rs67457459	BTN3A2	cis	Nerve Tibial	GTEx
rs67457459	BTN3A2	cis	Muscle Skeletal	GTEx
rs67457459	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs67457459	BTN3A2	cis	Esophagus Mucosa	GTEx
rs67457459	BTN3A2	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27193200-27198600	Weak transcription	GM12878-XiMat	blood
2	chr6:27196200-27199800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:27196400-27198600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27196800-27199600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:27196800-27200200	Active TSS	A549	lung
6	chr6:27197000-27198600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27197000-27199200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:27197000-27199400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:27197000-27199600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:27197000-27199600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:27197000-27200400	Active TSS	K562	blood
12	chr6:27197200-27198600	Active TSS	HMEC	breast
13	chr6:27197200-27199000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:27197200-27199000	Active TSS	NHEK	skin
15	chr6:27197200-27199200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:27197200-27199400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:27197200-27199400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:27197400-27198400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:27197400-27198600	Enhancers	Osteobl	bone
20	chr6:27197400-27198800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:27197400-27198800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:27197400-27198800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:27197400-27199000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:27197400-27199400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:27197400-27199400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:27197400-27199600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:27197400-27199600	Active TSS	Placenta	Placenta
28	chr6:27197400-27199800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr6:27197600-27198600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:27197600-27198600	Bivalent/Poised TSS	HepG2	liver
31	chr6:27197600-27198800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:27197600-27199400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:27198000-27199200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:27198200-27198400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr6:27198200-27198400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:27198200-27198400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
37	chr6:27198200-27198800	Active TSS	HSMM	muscle
38	chr6:27198200-27199800	Active TSS	Hela-S3	cervix

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