Variant report

Variant	rs3132389
Chromosome Location	chr6:28831021-28831022
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28803282..28808663-chr6:28829877..28836776,13	K562	blood:
2	chr6:27859769..27862740-chr6:28829876..28831991,2	K562	blood:
3	chr6:28803282..28808495-chr6:28830531..28834946,8	K562	blood:
4	chr6:28830168..28831847-chr6:28972589..28974401,2	K562	blood:
5	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
6	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
7	chr6:28830568..28832864-chr6:28971652..28974126,2	K562	blood:
8	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1233579	0.80[EUR][1000 genomes]
rs1233580	0.80[EUR][1000 genomes]
rs1233581	0.80[EUR][1000 genomes]
rs1233583	0.80[EUR][1000 genomes]
rs1233593	0.80[EUR][1000 genomes]
rs1233594	0.80[EUR][1000 genomes]
rs1233599	0.84[EUR][1000 genomes]
rs1233600	0.84[EUR][1000 genomes]
rs1233604	0.84[EUR][1000 genomes]
rs1233618	0.84[EUR][1000 genomes]
rs1233620	0.84[EUR][1000 genomes]
rs1233623	0.84[EUR][1000 genomes]
rs1238262	0.80[EUR][1000 genomes]
rs1311912	0.80[EUR][1000 genomes]
rs1311913	0.80[EUR][1000 genomes]
rs13206458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3117146	0.96[EUR][1000 genomes]
rs3118357	1.00[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3118364	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3118365	0.94[EUR][1000 genomes]
rs3118366	0.98[EUR][1000 genomes]
rs3118367	1.00[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3130838	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.98[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131073	0.93[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131081	0.96[EUR][1000 genomes]
rs3131093	0.98[EUR][1000 genomes]
rs3131094	1.00[EUR][1000 genomes]
rs3131095	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131096	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131097	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131101	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131335	0.98[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131340	0.89[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131343	0.87[EUR][1000 genomes]
rs3131345	1.00[EUR][1000 genomes]
rs3132373	0.87[EUR][1000 genomes]
rs3132374	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132376	1.00[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132384	1.00[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132387	0.98[EUR][1000 genomes]
rs3132388	1.00[EUR][1000 genomes]
rs3132391	1.00[EUR][1000 genomes]
rs3132392	1.00[EUR][1000 genomes]
rs3132393	0.98[EUR][1000 genomes]
rs3132394	0.98[EUR][1000 genomes]
rs3132395	0.98[EUR][1000 genomes]
rs3132396	0.89[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135294	0.87[EUR][1000 genomes]
rs3135295	1.00[EUR][1000 genomes]
rs3135297	0.94[EUR][1000 genomes]
rs3135298	0.98[EUR][1000 genomes]
rs3135299	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135300	1.00[EUR][1000 genomes]
rs3135302	1.00[EUR][1000 genomes]
rs3135304	1.00[EUR][1000 genomes]
rs3135306	1.00[EUR][1000 genomes]
rs3135307	1.00[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135309	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135310	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135311	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135312	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135313	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs35044849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35243068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4324798	0.89[EUR][1000 genomes]
rs7760313	0.98[EUR][1000 genomes]
rs7761321	0.87[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs7766699	0.84[EUR][1000 genomes]
rs7767099	0.87[EUR][1000 genomes]
rs9257133	0.80[EUR][1000 genomes]
rs9257136	0.80[EUR][1000 genomes]
rs9257137	0.80[EUR][1000 genomes]
rs9257140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257167	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9257183	0.84[EUR][1000 genomes]
rs9257184	0.84[EUR][1000 genomes]
rs9257187	0.84[EUR][1000 genomes]
rs9257188	0.84[EUR][1000 genomes]
rs9257189	0.84[EUR][1000 genomes]
rs9257192	0.84[EUR][1000 genomes]
rs9257217	0.87[EUR][1000 genomes]
rs9257223	0.89[EUR][1000 genomes]
rs9257227	0.85[EUR][1000 genomes]
rs9257245	0.98[EUR][1000 genomes]
rs9257249	0.96[EUR][1000 genomes]
rs9257250	0.96[EUR][1000 genomes]
rs9257262	1.00[EUR][1000 genomes]
rs9257267	0.96[EUR][1000 genomes]
rs9257272	1.00[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257345	0.87[AMR][1000 genomes];0.89[EUR][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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
4	esv3403240	chr6:28808022-28832799	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3132389	BTN3A2	trans	lymphoblastoid	seeQTL
rs3132389	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3132389	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3132389	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28829600-28831400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:28829800-28831200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:28830200-28831200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:28830400-28832200	Active TSS	Hela-S3	cervix
5	chr6:28830400-28833000	Active TSS	Fetal Brain Female	brain
6	chr6:28830600-28831400	Flanking Active TSS	Dnd41	blood
7	chr6:28830600-28832200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:28830600-28832200	Active TSS	Brain Anterior Caudate	brain
9	chr6:28830600-28832200	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:28830600-28834800	Active TSS	A549	lung
11	chr6:28830800-28831200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:28830800-28831200	Enhancers	Primary T cells from cord blood	blood
13	chr6:28830800-28831200	Bivalent Enhancer	Fetal Thymus	thymus
14	chr6:28830800-28831200	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr6:28830800-28831400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr6:28830800-28831400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr6:28830800-28831400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr6:28830800-28832200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:28830800-28832200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:28830800-28832200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr6:28830800-28832200	Active TSS	Brain Substantia Nigra	brain
22	chr6:28830800-28832400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr6:28830800-28832400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:28830800-28832400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:28830800-28832400	Active TSS	Fetal Brain Male	brain
26	chr6:28830800-28832600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr6:28830800-28832600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr6:28831000-28831200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:28831000-28831200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:28831000-28831200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:28831000-28831200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:28831000-28831200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:28831000-28831200	Enhancers	Liver	Liver
34	chr6:28831000-28831200	Enhancers	Fetal Muscle Leg	muscle
35	chr6:28831000-28831200	Enhancers	Placenta	Placenta
36	chr6:28831000-28831200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
37	chr6:28831000-28831200	Enhancers	NHEK	skin
38	chr6:28831000-28831400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:28831000-28831400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr6:28831000-28831400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:28831000-28831400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:28831000-28831400	Flanking Active TSS	GM12878-XiMat	blood
43	chr6:28831000-28831400	Flanking Active TSS	HepG2	liver
44	chr6:28831000-28831400	Flanking Active TSS	HMEC	breast
45	chr6:28831000-28831400	Flanking Active TSS	HUVEC	blood vessel
46	chr6:28831000-28831400	Flanking Active TSS	K562	blood
47	chr6:28831000-28831400	Flanking Active TSS	Osteobl	bone
48	chr6:28831000-28831600	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr6:28831000-28832000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:28831000-28832000	Active TSS	Primary T helper cells PMA-I stimulated	--

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