Variant report

Variant	rs66757203
Chromosome Location	chr6:26454956-26454957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26202174..26206210-chr6:26451824..26455536,3	K562	blood:
2	chr6:26449553..26453974-chr6:26454911..26459271,5	K562	blood:
3	chr6:26419843..26421610-chr6:26453709..26456222,2	K562	blood:

Variant related genes	Relation type
ENSG00000217275	Chromatin interaction
ENSG00000111801	Chromatin interaction
ENSG00000198518	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13195402	0.91[AMR][1000 genomes]
rs13195509	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220261	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220495	0.83[EUR][1000 genomes]
rs34104395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34148261	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34246779	0.89[EUR][1000 genomes]
rs34605993	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277236	0.89[EUR][1000 genomes]
rs35433030	0.98[EUR][1000 genomes]
rs35555795	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35627490	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35680819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36033628	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36162392	0.85[EUR][1000 genomes]
rs3734542	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734543	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734545	0.86[ASN][1000 genomes]
rs3823158	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266839	0.85[EUR][1000 genomes]
rs66941101	0.98[EUR][1000 genomes]
rs71557340	0.90[EUR][1000 genomes]
rs72843784	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72844462	0.89[EUR][1000 genomes]
rs72845428	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
4	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
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	esv2763996	chr6:26423901-26465384	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1017824	chr6:26425410-26465384	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1030289	chr6:26428314-26464017	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1033003	chr6:26428314-26465384	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv1031229	chr6:26428314-26467182	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1031238	chr6:26428314-26471596	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1024483	chr6:26429262-26465384	Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv1034561	chr6:26429262-26467182	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv528172	chr6:26430981-26463660	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
16	nsv1029357	chr6:26432815-26464789	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
17	nsv1023581	chr6:26432815-26465384	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
18	nsv1024222	chr6:26432815-26467182	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1022309	chr6:26434914-26464789	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs66757203	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs66757203	BTN3A2	cis	Artery Aorta	GTEx
rs66757203	BTN3A2	cis	Nerve Tibial	GTEx
rs66757203	BTN3A2	cis	Muscle Skeletal	GTEx
rs66757203	BTN3A2	cis	Whole Blood	GTEx
rs66757203	BTN3A2	cis	Esophagus Muscularis	GTEx
rs66757203	BTN3A2	cis	Thyroid	GTEx
rs66757203	BTN3A2	cis	Stomach	GTEx
rs66757203	BTN3A2	cis	lung	GTEx
rs66757203	BTN3A2	cis	Esophagus Mucosa	GTEx
rs66757203	BTN3A2	cis	Heart Left Ventricle	GTEx
rs66757203	BTN3A2	cis	Artery Tibial	GTEx
rs66757203	BTN3A2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26441200-26457000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:26441200-26457600	Weak transcription	Pancreas	Pancrea
3	chr6:26441400-26455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:26441400-26457000	Weak transcription	Brain Anterior Caudate	brain
5	chr6:26441400-26457400	Weak transcription	Psoas Muscle	Psoas
6	chr6:26442200-26455800	Weak transcription	HepG2	liver
7	chr6:26442200-26457400	Weak transcription	Fetal Kidney	kidney
8	chr6:26442400-26457400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:26442400-26457400	Weak transcription	Hela-S3	cervix
10	chr6:26442600-26457400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:26443000-26457400	Weak transcription	Stomach Mucosa	stomach
12	chr6:26445200-26457400	Weak transcription	Small Intestine	intestine
13	chr6:26446400-26457200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:26446400-26457400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:26446400-26458200	Weak transcription	Gastric	stomach
16	chr6:26446600-26457000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:26448000-26457600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:26448400-26456800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr6:26449000-26457600	Weak transcription	Right Ventricle	heart
20	chr6:26449200-26457400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:26449400-26457400	Weak transcription	HUVEC	blood vessel
22	chr6:26449800-26456600	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:26450000-26456800	Weak transcription	Esophagus	oesophagus
24	chr6:26450200-26457400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:26450400-26456800	Weak transcription	Aorta	Aorta
26	chr6:26450400-26457400	Weak transcription	Thymus	Thymus
27	chr6:26450600-26455400	Weak transcription	GM12878-XiMat	blood
28	chr6:26450600-26456800	Weak transcription	Left Ventricle	heart
29	chr6:26450600-26457400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:26450800-26457200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:26450800-26457400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:26450800-26457600	Weak transcription	Placenta	Placenta
33	chr6:26450800-26458200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:26451000-26457400	Weak transcription	Primary B cells from cord blood	blood
35	chr6:26451000-26457400	Weak transcription	Fetal Intestine Large	intestine
36	chr6:26451000-26457600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:26451200-26456600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:26451400-26456800	Weak transcription	Dnd41	blood
39	chr6:26451400-26457400	Weak transcription	Fetal Lung	lung
40	chr6:26451400-26457600	Weak transcription	Ovary	ovary
41	chr6:26451800-26457600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:26452000-26455400	Weak transcription	Lung	lung
43	chr6:26452000-26456800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:26452000-26456800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:26452000-26457200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:26452000-26457400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:26452000-26457400	Weak transcription	Adipose Nuclei	Adipose
48	chr6:26452000-26457400	Weak transcription	Liver	Liver
49	chr6:26452000-26457400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:26452000-26457400	Weak transcription	Rectal Mucosa Donor 29	rectum

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