Variant report

Variant	rs4324798
Chromosome Location	chr6:28776117-28776118
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28774872..28779186-chr6:28780865..28786550,9	K562	blood:
2	chr6:28723125..28726078-chr6:28775767..28777359,2	K562	blood:
3	chr6:28760359..28762539-chr6:28774291..28776179,2	K562	blood:
4	chr6:28768996..28771268-chr6:28774440..28778213,3	K562	blood:
5	chr6:28775179..28778043-chr6:28889400..28891921,3	MCF-7	breast:
6	chr6:28760359..28764219-chr6:28771578..28776179,5	K562	blood:
7	chr6:28774860..28778003-chr6:28805367..28807894,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-18	chr6:28773744-28776603	NONHSAT108486

No data

Variant related genes	Relation type
ENSG00000265764	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1233579	0.84[EUR][1000 genomes]
rs1233580	0.84[EUR][1000 genomes]
rs1233581	0.84[EUR][1000 genomes]
rs1233583	0.84[EUR][1000 genomes]
rs1233593	0.84[EUR][1000 genomes]
rs1233594	0.84[EUR][1000 genomes]
rs1233599	0.87[EUR][1000 genomes]
rs1233600	0.87[EUR][1000 genomes]
rs1233604	0.87[EUR][1000 genomes]
rs1233618	0.87[EUR][1000 genomes]
rs1233620	0.87[EUR][1000 genomes]
rs1233623	0.87[EUR][1000 genomes]
rs1238262	0.84[EUR][1000 genomes]
rs1311911	0.82[EUR][1000 genomes]
rs1311912	0.84[EUR][1000 genomes]
rs1311913	0.84[EUR][1000 genomes]
rs13206458	0.85[EUR][1000 genomes]
rs13437309	0.86[AFR][1000 genomes]
rs1742743	0.82[EUR][1000 genomes]
rs3118357	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3118359	0.89[EUR][1000 genomes]
rs3118360	0.96[EUR][1000 genomes]
rs3118361	0.85[EUR][1000 genomes]
rs3118364	0.84[EUR][1000 genomes]
rs3118365	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3118366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3118367	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130837	0.89[EUR][1000 genomes]
rs3130838	0.89[EUR][1000 genomes]
rs3130844	0.85[EUR][1000 genomes]
rs3130845	0.85[EUR][1000 genomes]
rs3130846	0.82[EUR][1000 genomes]
rs3130847	0.85[EUR][1000 genomes]
rs3130885	0.83[EUR][1000 genomes]
rs3130887	0.87[EUR][1000 genomes]
rs3130888	0.85[EUR][1000 genomes]
rs3130892	0.85[EUR][1000 genomes]
rs3130895	0.84[EUR][1000 genomes]
rs3131068	0.85[EUR][1000 genomes]
rs3131069	0.85[EUR][1000 genomes]
rs3131071	0.85[EUR][1000 genomes]
rs3131072	0.85[EUR][1000 genomes]
rs3131073	0.82[EUR][1000 genomes]
rs3131075	0.85[EUR][1000 genomes]
rs3131076	0.85[EUR][1000 genomes]
rs3131093	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131094	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131095	0.89[EUR][1000 genomes]
rs3131096	0.89[EUR][1000 genomes]
rs3131097	0.89[EUR][1000 genomes]
rs3131101	0.81[EUR][1000 genomes]
rs3131335	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131336	0.89[EUR][1000 genomes]
rs3131340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131341	1.00[EUR][1000 genomes]
rs3131343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3131345	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132374	0.85[EUR][1000 genomes]
rs3132376	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132378	0.81[EUR][1000 genomes]
rs3132382	0.85[EUR][1000 genomes]
rs3132384	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132385	0.89[EUR][1000 genomes]
rs3132387	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132388	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132389	0.89[EUR][1000 genomes]
rs3132391	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132393	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132394	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135293	0.89[EUR][1000 genomes]
rs3135294	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135297	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3135298	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3135299	0.85[EUR][1000 genomes]
rs3135300	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135302	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135304	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135306	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135307	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135308	0.89[EUR][1000 genomes]
rs3135309	0.89[EUR][1000 genomes]
rs3135310	0.89[EUR][1000 genomes]
rs3135311	0.89[EUR][1000 genomes]
rs3135312	0.89[EUR][1000 genomes]
rs3135313	0.89[EUR][1000 genomes]
rs3135316	0.89[EUR][1000 genomes]
rs3135318	0.85[EUR][1000 genomes]
rs3135325	0.85[EUR][1000 genomes]
rs6928657	0.90[AFR][1000 genomes]
rs7745088	0.83[AFR][1000 genomes]
rs7760313	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7761321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7764642	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7766699	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7767099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257133	0.84[EUR][1000 genomes]
rs9257136	0.84[EUR][1000 genomes]
rs9257137	0.84[EUR][1000 genomes]
rs9257140	0.84[EUR][1000 genomes]
rs9257167	0.87[EUR][1000 genomes]
rs9257183	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257184	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257187	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257188	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257189	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257192	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257227	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257245	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257249	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257250	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9257267	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257272	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9257331	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3384463	chr6:28759027-28776259	Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2621756	chr6:28762692-28779791	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2322180	chr6:28764675-28780578	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lung adenocarcinoma	19836008	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4324798	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs4324798	ZFP57	cis	lymphoblastoid	seeQTL
rs4324798	BTN3A2	trans	lymphoblastoid	seeQTL
rs4324798	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs4324798	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28775200-28778200	Weak transcription	Right Atrium	heart
2	chr6:28775600-28776200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:28775600-28776200	Active TSS	NHEK	skin
4	chr6:28775600-28776400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:28775600-28776400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:28775600-28776400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:28775600-28776400	Bivalent/Poised TSS	HUVEC	blood vessel
8	chr6:28775600-28776400	Active TSS	NH-A	brain
9	chr6:28775600-28776400	Active TSS	NHLF	lung
10	chr6:28775600-28776600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr6:28775600-28776600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:28775600-28776600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:28775600-28776600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:28775600-28776600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr6:28775600-28776600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:28775600-28776600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:28775600-28776600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:28775600-28776600	Active TSS	K562	blood
19	chr6:28775600-28776800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr6:28775600-28776800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:28775600-28776800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:28775600-28776800	Active TSS	Hela-S3	cervix
23	chr6:28775600-28777000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:28775600-28778600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr6:28775600-28778600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:28775800-28776200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:28775800-28776200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:28775800-28776200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:28775800-28776200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:28775800-28776200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:28775800-28776200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:28775800-28776200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:28775800-28776200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr6:28775800-28776200	Active TSS	A549	lung
35	chr6:28775800-28776200	Flanking Active TSS	GM12878-XiMat	blood
36	chr6:28775800-28776200	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr6:28775800-28776200	Active TSS	HSMMtube	muscle
38	chr6:28775800-28776200	Flanking Active TSS	Osteobl	bone
39	chr6:28775800-28776400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:28775800-28776400	Flanking Active TSS	HMEC	breast
41	chr6:28775800-28776400	Bivalent/Poised TSS	NHDF-Ad	bronchial
42	chr6:28775800-28776600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr6:28775800-28776600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
44	chr6:28776000-28776200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
45	chr6:28776000-28776200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:28776000-28776200	Active TSS	HSMM	muscle
47	chr6:28776000-28776400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr6:28776000-28776400	Bivalent/Poised TSS	Adipose Nuclei	Adipose

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