Variant report

Variant	rs9467989
Chromosome Location	chr6:27064275-27064276
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27063517..27066449-chr6:27068447..27070527,3	K562	blood:
2	chr6:27063847..27066118-chr6:27098069..27100719,2	K562	blood:
3	chr6:26922448..26924229-chr6:27062597..27064654,2	K562	blood:
4	chr6:27062755..27066396-chr6:27068240..27071755,4	K562	blood:
5	chr6:27062735..27064770-chr6:27065188..27068099,2	K562	blood:
6	chr6:26574454..26577093-chr6:27063520..27065530,2	K562	blood:
7	chr6:27059758..27061626-chr6:27062610..27064960,3	MCF-7	breast:
8	chr6:26283850..26285980-chr6:27064223..27066253,2	MCF-7	breast:
9	chr6:27054006..27058135-chr6:27062347..27065420,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000158406	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs6916301	0.99[ASN][1000 genomes]
rs6933999	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73401108	0.96[ASN][1000 genomes]
rs73401117	0.96[ASN][1000 genomes]
rs7745603	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7761889	0.96[ASN][1000 genomes]
rs9357031	0.99[ASN][1000 genomes]
rs9368489	0.85[AMR][1000 genomes]
rs9379961	0.85[AMR][1000 genomes]
rs9379962	0.84[AMR][1000 genomes]
rs994690	0.84[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	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9467989	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9467989	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9467989	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27060200-27064600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:27060400-27064400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27063800-27064400	Weak transcription	Right Atrium	heart
4	chr6:27063800-27064600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:27063800-27065000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:27063800-27065600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr6:27064000-27064400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:27064000-27064400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:27064000-27064600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:27064000-27064600	Flanking Active TSS	HMEC	breast
11	chr6:27064000-27064800	Active TSS	K562	blood
12	chr6:27064000-27065600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:27064000-27065600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:27064000-27065600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:27064000-27066600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:27064200-27064400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:27064200-27064400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr6:27064200-27064400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
19	chr6:27064200-27064400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:27064200-27064400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:27064200-27064400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:27064200-27064400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr6:27064200-27064400	Enhancers	HSMM	muscle
24	chr6:27064200-27064400	Enhancers	HSMMtube	muscle
25	chr6:27064200-27064400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
26	chr6:27064200-27064400	Flanking Bivalent TSS/Enh	NH-A	brain
27	chr6:27064200-27064400	Bivalent/Poised TSS	NHDF-Ad	bronchial
28	chr6:27064200-27064400	Flanking Active TSS	NHLF	lung
29	chr6:27064200-27064400	Flanking Bivalent TSS/Enh	Osteobl	bone
30	chr6:27064200-27064600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:27064200-27064600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:27064200-27064600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
33	chr6:27064200-27064600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:27064200-27064600	Active TSS	Lung	lung
35	chr6:27064200-27064600	Flanking Active TSS	NHEK	skin
36	chr6:27064200-27065200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:27064200-27065200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:27064200-27065200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
39	chr6:27064200-27065400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:27064200-27065400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:27064200-27065400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:27064200-27065400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:27064200-27065400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:27064200-27065400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:27064200-27065400	Active TSS	A549	lung
46	chr6:27064200-27065600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:27064200-27065600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr6:27064200-27065600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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