Variant report

Variant	rs56296968
Chromosome Location	chr6:26474571-26474572
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26474445..26476878-chr6:26512542..26515226,3	K562	blood:
2	chr6:26457588..26459634-chr6:26472542..26475354,3	MCF-7	breast:
3	chr6:26472114..26481394-chr6:26482721..26495847,23	K562	blood:
4	chr6:26474221..26477564-chr6:26521186..26523081,3	K562	blood:
5	chr6:26469351..26470926-chr6:26472067..26474626,2	K562	blood:
6	chr11:62609018..62609547-chr6:26474168..26475039,2	NB4	blood:
7	chr6:26314124..26316500-chr6:26474166..26476547,2	K562	blood:
8	chr6:26474337..26476257-chr6:26519630..26521866,2	MCF-7	breast:
9	chr6:26382919..26385188-chr6:26473437..26474979,2	K562	blood:
10	chr6:26342125..26345094-chr6:26474079..26475850,2	K562	blood:
11	chr6:26473312..26475713-chr6:26519494..26521271,2	MCF-7	breast:
12	chr6:26343594..26345212-chr6:26474079..26475915,2	K562	blood:
13	chr6:26474090..26476155-chr6:26476306..26478036,2	MCF-7	breast:
14	chr6:26471319..26475410-chr6:26567164..26571952,5	K562	blood:
15	chr6:26324380..26326185-chr6:26473831..26475753,2	K562	blood:
16	chr6:26472961..26477109-chr6:26519664..26522390,3	K562	blood:
17	chr6:26456009..26458208-chr6:26473841..26475463,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112763	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000124508	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12176129	0.85[ASN][1000 genomes]
rs13195047	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16891717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891725	0.98[ASN][1000 genomes]
rs2093169	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295593	0.85[ASN][1000 genomes]
rs2393657	0.86[ASN][1000 genomes]
rs2393665	0.86[ASN][1000 genomes]
rs34313099	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799380	0.91[EUR][1000 genomes]
rs3799383	0.85[ASN][1000 genomes]
rs4518487	0.91[EUR][1000 genomes]
rs6456727	0.91[EUR][1000 genomes]
rs6456728	0.86[EUR][1000 genomes]
rs67234939	0.85[ASN][1000 genomes]
rs6900665	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6911765	0.86[ASN][1000 genomes]
rs6924727	0.86[EUR][1000 genomes]
rs6926677	0.87[EUR][1000 genomes]
rs6933213	0.86[EUR][1000 genomes]
rs6941920	0.86[EUR][1000 genomes]
rs7756567	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348718	0.86[ASN][1000 genomes]
rs9348719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348720	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348721	0.94[ASN][1000 genomes]
rs9357007	0.86[ASN][1000 genomes]
rs9358944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358946	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358947	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358948	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379877	0.87[ASN][1000 genomes]
rs9379880	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379882	0.85[ASN][1000 genomes]
rs9393725	0.81[ASN][1000 genomes]
rs9393727	0.85[ASN][1000 genomes]
rs9467772	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs56296968	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs56296968	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs56296968	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs56296968	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs56296968	BTN3A2	cis	Artery Tibial	GTEx
rs56296968	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs56296968	BTN3A2	cis	Whole Blood	GTEx
rs56296968	BTN3A2	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26469600-26476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:26471800-26474600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:26471800-26474600	Weak transcription	Esophagus	oesophagus
4	chr6:26471800-26474800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:26471800-26474800	Weak transcription	Small Intestine	intestine
6	chr6:26471800-26475000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:26471800-26475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:26471800-26476400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:26471800-26478000	Weak transcription	Lung	lung
10	chr6:26473200-26475200	Weak transcription	Spleen	Spleen
11	chr6:26473400-26474800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:26473400-26475000	Active TSS	Stomach Smooth Muscle	stomach
13	chr6:26473600-26474600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:26473600-26474600	Active TSS	HMEC	breast
15	chr6:26473600-26474600	Active TSS	NHEK	skin
16	chr6:26473600-26474800	Active TSS	Primary T cells fromperipheralblood	blood
17	chr6:26473600-26474800	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr6:26473600-26474800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:26473600-26474800	Active TSS	Brain Hippocampus Middle	brain
20	chr6:26473600-26474800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr6:26473600-26474800	Active TSS	Fetal Lung	lung
22	chr6:26473600-26474800	Active TSS	Fetal Muscle Leg	muscle
23	chr6:26473600-26474800	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr6:26473600-26474800	Active TSS	NHDF-Ad	bronchial
25	chr6:26473600-26474800	Active TSS	Osteobl	bone
26	chr6:26473600-26475000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:26473600-26475000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:26473600-26475200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:26473600-26475200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:26473600-26475400	Active TSS	A549	lung
31	chr6:26473600-26475400	Active TSS	HSMMtube	muscle
32	chr6:26473600-26476400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:26473800-26474600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:26473800-26474600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:26473800-26474600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:26473800-26474600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:26473800-26474600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:26473800-26474600	Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr6:26473800-26474600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:26473800-26474600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:26473800-26474600	Active TSS	Adipose Nuclei	Adipose
42	chr6:26473800-26474600	Active TSS	Liver	Liver
43	chr6:26473800-26474600	Active TSS	Brain Anterior Caudate	brain
44	chr6:26473800-26474600	Active TSS	Fetal Intestine Small	intestine
45	chr6:26473800-26474600	Active TSS	Fetal Thymus	thymus
46	chr6:26473800-26474600	Active TSS	Hela-S3	cervix
47	chr6:26473800-26474600	Active TSS	HUVEC	blood vessel
48	chr6:26473800-26474600	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:26473800-26474600	Active TSS	NH-A	brain
50	chr6:26473800-26474800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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