Variant report

Variant	rs6939799
Chromosome Location	chr6:26328366-26328367
allele	A/G
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:0)
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	chr6:26286019..26289232-chr6:26328153..26331757,3	MCF-7	breast:
2	chr6:26327533..26330637-chr6:27103047..27105272,3	K562	blood:
3	chr6:26328264..26330441-chr6:27085244..27087938,2	K562	blood:
4	chr6:26327922..26330114-chr6:26594623..26596839,2	K562	blood:
5	chr6:26317773..26322423-chr6:26326646..26329657,4	MCF-7	breast:
6	chr6:26326957..26329789-chr6:26556896..26559619,2	MCF-7	breast:
7	chr6:26323417..26326776-chr6:26326785..26329865,3	MCF-7	breast:
8	chr6:26322866..26325773-chr6:26327005..26329096,3	MCF-7	breast:
9	chr6:26327970..26330676-chr6:26575820..26578738,2	K562	blood:
10	chr6:26327903..26334280-chr6:26553526..26557732,8	K562	blood:
11	chr6:26321015..26322642-chr6:26328145..26329950,2	MCF-7	breast:
12	chr6:26325742..26329401-chr6:26567650..26570455,4	K562	blood:
13	chr6:26325462..26328933-chr6:26567431..26570210,5	K562	blood:
14	chr6:26327534..26329302-chr6:27101295..27103250,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000220875	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11962660	1.00[ASN][1000 genomes]
rs1883215	1.00[ASN][1000 genomes]
rs34569761	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6456710	0.82[ASN][1000 genomes]
rs6902389	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6902392	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6903015	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6908156	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6910374	0.89[ASN][1000 genomes]
rs6923139	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6939978	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7745232	0.89[ASN][1000 genomes]
rs9467699	1.00[ASN][1000 genomes]
rs9467700	1.00[ASN][1000 genomes]
rs9467701	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467704	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467707	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467708	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9467709	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
7	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6939799	BTN3A2	cis	Thyroid	GTEx
rs6939799	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs6939799	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs6939799	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26322800-26331200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26326600-26332800	Active TSS	A549	lung
3	chr6:26326800-26329000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:26326800-26329000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:26326800-26329000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:26326800-26329400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:26326800-26329600	Active TSS	K562	blood
8	chr6:26326800-26330200	Active TSS	GM12878-XiMat	blood
9	chr6:26327000-26328800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:26327000-26329000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:26327000-26329000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:26327000-26329200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:26327000-26329400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:26327000-26329400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:26327000-26329400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:26327000-26331800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr6:26327200-26328400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:26327200-26328400	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr6:26327200-26328800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:26327200-26328800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:26327200-26328800	Active TSS	HMEC	breast
22	chr6:26327200-26329000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:26327200-26329000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:26327200-26329000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:26327200-26329000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:26327200-26329000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr6:26327200-26329400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:26327200-26329400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:26327200-26333000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:26327400-26328400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:26327400-26328400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:26327400-26328400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
33	chr6:26327400-26328400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
34	chr6:26327400-26328800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:26327400-26329000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr6:26327400-26329000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:26327400-26329000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:26327400-26329200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:26327400-26329200	Active TSS	NH-A	brain
40	chr6:26327400-26329400	Active TSS	NHLF	lung
41	chr6:26327400-26329400	Active TSS	Osteobl	bone
42	chr6:26327400-26329800	Active TSS	Hela-S3	cervix
43	chr6:26327400-26331000	Active TSS	NHEK	skin
44	chr6:26327600-26328400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
45	chr6:26327600-26328800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:26327600-26328800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:26327600-26328800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr6:26327600-26328800	Active TSS	Placenta	Placenta
49	chr6:26327600-26329000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:26327800-26328400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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