Variant report

Variant	rs3135302
Chromosome Location	chr6:28829637-28829638
allele	C/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:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28827198..28830005-chr6:28973058..28974944,2	K562	blood:
2	chr6:28806019..28808869-chr6:28827811..28829720,2	K562	blood:
3	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
4	chr6:28804491..28806748-chr6:28829481..28831000,2	MCF-7	breast:
5	chr6:28806762..28809202-chr6:28828058..28830893,2	MCF-7	breast:
6	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-3	chr6:28827402-28829792	ENSG00000225595
2	lnc-TRIM27-3	chr6:28828927-28829792	ENSG00000225595.2
3	lnc-TRIM27-3	chr6:28827402-28829792	NONHSAT108488

No data

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000197935	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:131)

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	0.96[EUR][1000 genomes]
rs13437309	0.90[AFR][1000 genomes]
rs3117146	0.96[EUR][1000 genomes]
rs3118357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3118359	1.00[EUR][1000 genomes]
rs3118360	0.92[EUR][1000 genomes]
rs3118361	0.96[EUR][1000 genomes]
rs3118364	0.95[EUR][1000 genomes]
rs3118365	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3118366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3118367	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129791	0.89[EUR][1000 genomes]
rs3129794	0.96[EUR][1000 genomes]
rs3129797	0.96[EUR][1000 genomes]
rs3129798	0.96[EUR][1000 genomes]
rs3130837	1.00[EUR][1000 genomes]
rs3130838	1.00[EUR][1000 genomes]
rs3130844	0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	0.93[EUR][1000 genomes]
rs3130847	0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.98[EUR][1000 genomes]
rs3130888	0.96[EUR][1000 genomes]
rs3130890	0.85[EUR][1000 genomes]
rs3130891	0.96[EUR][1000 genomes]
rs3130892	0.96[EUR][1000 genomes]
rs3130893	0.96[EUR][1000 genomes]
rs3130894	0.96[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	0.96[EUR][1000 genomes]
rs3131068	0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	0.96[EUR][1000 genomes]
rs3131072	0.96[EUR][1000 genomes]
rs3131073	0.93[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	0.96[EUR][1000 genomes]
rs3131081	0.96[EUR][1000 genomes]
rs3131093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3131094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131095	1.00[EUR][1000 genomes]
rs3131096	1.00[EUR][1000 genomes]
rs3131097	1.00[EUR][1000 genomes]
rs3131101	0.92[EUR][1000 genomes]
rs3131335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3131336	1.00[EUR][1000 genomes]
rs3131340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131341	0.89[EUR][1000 genomes]
rs3131343	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3131345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132374	0.96[EUR][1000 genomes]
rs3132376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132378	0.92[EUR][1000 genomes]
rs3132382	0.96[EUR][1000 genomes]
rs3132384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132385	1.00[EUR][1000 genomes]
rs3132387	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132388	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132389	1.00[EUR][1000 genomes]
rs3132391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135293	1.00[EUR][1000 genomes]
rs3135294	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3135295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135297	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135298	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135299	0.96[EUR][1000 genomes]
rs3135300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135308	1.00[EUR][1000 genomes]
rs3135309	1.00[EUR][1000 genomes]
rs3135310	1.00[EUR][1000 genomes]
rs3135311	1.00[EUR][1000 genomes]
rs3135312	1.00[EUR][1000 genomes]
rs3135313	1.00[EUR][1000 genomes]
rs3135316	1.00[EUR][1000 genomes]
rs3135317	0.96[EUR][1000 genomes]
rs3135318	0.96[EUR][1000 genomes]
rs3135325	0.96[EUR][1000 genomes]
rs4324798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6928657	0.86[AFR][1000 genomes]
rs7760313	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7761321	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7764642	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7766699	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7767099	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9257133	0.80[EUR][1000 genomes]
rs9257136	0.80[EUR][1000 genomes]
rs9257137	0.80[EUR][1000 genomes]
rs9257140	0.80[EUR][1000 genomes]
rs9257167	0.84[EUR][1000 genomes]
rs9257183	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257184	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257187	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257188	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257189	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257192	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257217	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9257223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9257227	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257245	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9257249	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257331	1.00[EUR][1000 genomes]
rs9257345	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3135302	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3135302	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3135302	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28825400-28830200	Weak transcription	K562	blood
2	chr6:28828400-28830800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:28828800-28829800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28829000-28830000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:28829400-28830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:28829600-28831000	Weak transcription	HMEC	breast
7	chr6:28829600-28831400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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