Variant report

Variant	rs28362606
Chromosome Location	chr6:26365586-26365587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26364672..26366648-chr6:26519902..26522691,2	K562	blood:
2	chr6:26363140..26366680-chr6:26382117..26385194,3	MCF-7	breast:
3	chr6:26365183..26366783-chr6:26383299..26386049,2	K562	blood:
4	chr6:26360935..26366570-chr6:26520779..26523276,5	K562	blood:

Variant related genes	Relation type
ENSG00000228223	Chromatin interaction
ENSG00000124508	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs12173854	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174602	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174623	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174631	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12174639	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12176317	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13191660	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13216828	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16891725	0.81[EUR][1000 genomes]
rs1977	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1978	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1979	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2072803	0.87[EUR][1000 genomes]
rs2072806	0.87[EUR][1000 genomes]
rs2073527	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073529	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073530	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073531	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076030	0.87[EUR][1000 genomes]
rs2235251	0.86[EUR][1000 genomes]
rs2393667	0.86[EUR][1000 genomes]
rs28551159	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3047288	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34273322	0.86[EUR][1000 genomes]
rs34436535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34550936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34622023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35304979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35307327	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35934643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35942482	0.86[EUR][1000 genomes]
rs3757138	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58825580	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66823108	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66827971	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67509210	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68072215	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68112369	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900665	0.87[EUR][1000 genomes]
rs71544290	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71557332	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71557334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71557335	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841536	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9348709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348716	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348721	0.87[EUR][1000 genomes]
rs9357006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358935	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358937	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358938	0.87[EUR][1000 genomes]
rs9358939	0.86[EUR][1000 genomes]
rs9366653	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366654	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9366655	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9366656	0.86[EUR][1000 genomes]
rs9379850	0.92[ASN][1000 genomes]
rs9379851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379857	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379858	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379863	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379864	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379871	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379873	0.88[EUR][1000 genomes]
rs9379875	0.86[EUR][1000 genomes]
rs9393703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393710	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393711	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393713	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393714	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393715	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393718	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs28362606	BTN3A2	cis	Artery Aorta	GTEx
rs28362606	BTN3A2	cis	Esophagus Muscularis	GTEx
rs28362606	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs28362606	BTN3A2	cis	Thyroid	GTEx
rs28362606	BTN3A2	cis	Esophagus Mucosa	GTEx
rs28362606	BTN3A2	cis	Stomach	GTEx
rs28362606	BTN3A2	cis	Muscle Skeletal	GTEx
rs28362606	BTN3A2	cis	Artery Tibial	GTEx
rs28362606	BTN3A2	cis	Whole Blood	GTEx
rs28362606	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs28362606	BTN3A2	cis	lung	GTEx
rs28362606	BTN3A2	cis	Heart Left Ventricle	GTEx
rs28362606	BTN3A2	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26364200-26366000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:26364400-26365800	Active TSS	HSMM	muscle
3	chr6:26364400-26366000	Active TSS	Brain Anterior Caudate	brain
4	chr6:26364400-26366200	Active TSS	Stomach Smooth Muscle	stomach
5	chr6:26364600-26365800	Active TSS	Aorta	Aorta
6	chr6:26364600-26366000	Active TSS	Brain Substantia Nigra	brain
7	chr6:26364600-26366800	Active TSS	Right Atrium	heart
8	chr6:26364600-26366800	Active TSS	Right Ventricle	heart
9	chr6:26364800-26365600	Active TSS	Fetal Brain Male	brain
10	chr6:26364800-26365800	Active TSS	Fetal Brain Female	brain
11	chr6:26364800-26365800	Bivalent/Poised TSS	HepG2	liver
12	chr6:26364800-26366000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:26364800-26366000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:26364800-26366000	Active TSS	Brain Angular Gyrus	brain
15	chr6:26364800-26366000	Active TSS	Colonic Mucosa	Colon
16	chr6:26364800-26366000	Active TSS	Fetal Muscle Trunk	muscle
17	chr6:26364800-26366000	Active TSS	Fetal Stomach	stomach
18	chr6:26364800-26366000	Active TSS	Ovary	ovary
19	chr6:26364800-26366000	Active TSS	Psoas Muscle	Psoas
20	chr6:26364800-26366000	Active TSS	Stomach Mucosa	stomach
21	chr6:26364800-26366200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:26364800-26366200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:26364800-26366200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:26364800-26366200	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:26364800-26366200	Active TSS	Fetal Muscle Leg	muscle
26	chr6:26364800-26366200	Active TSS	Placenta	Placenta
27	chr6:26364800-26366200	Active TSS	A549	lung
28	chr6:26364800-26366200	Active TSS	HMEC	breast
29	chr6:26364800-26366400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:26364800-26366400	Active TSS	K562	blood
31	chr6:26364800-26366400	Active TSS	NHLF	lung
32	chr6:26364800-26366800	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:26364800-26366800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:26364800-26366800	Weak transcription	Spleen	Spleen
35	chr6:26364800-26367600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:26365000-26365600	Active TSS	Primary B cells from cord blood	blood
37	chr6:26365000-26365800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:26365000-26365800	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr6:26365000-26365800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:26365000-26365800	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr6:26365000-26365800	Active TSS	Liver	Liver
42	chr6:26365000-26365800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:26365000-26365800	Active TSS	Fetal Heart	heart
44	chr6:26365000-26365800	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:26365000-26365800	Active TSS	NHEK	skin
46	chr6:26365000-26366000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:26365000-26366000	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:26365000-26366000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:26365000-26366000	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr6:26365000-26366000	Active TSS	iPS-18 Cell Line	embryonic stem cell

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