Variant report

Variant	rs3135297
Chromosome Location	chr6:28804688-28804689
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28804491..28806748-chr6:28829481..28831000,2	MCF-7	breast:
2	chr6:28803400..28808440-chr6:28861740..28869149,12	K562	blood:
3	chr6:28710816..28712847-chr6:28804095..28806646,2	K562	blood:
4	chr6:28733597..28735281-chr6:28802392..28805024,2	K562	blood:
5	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
6	chr6:28802089..28805031-chr6:28809427..28811386,2	K562	blood:
7	chr6:28803282..28808663-chr6:28829877..28836776,13	K562	blood:
8	chr6:28803282..28808495-chr6:28830531..28834946,8	K562	blood:
9	chr6:28804571..28808832-chr6:28889803..28892525,4	MCF-7	breast:
10	chr6:28804431..28805980-chr6:28984572..28985541,9	MCF-7	breast:
11	chr6:28693769..28696400-chr6:28804513..28806706,3	K562	blood:
12	chr6:28804427..28806431-chr6:28981603..28983162,2	K562	blood:
13	chr6:28804320..28805825-chr6:28984205..28985476,10	K562	blood:
14	chr6:28804076..28806200-chr6:28922392..28924838,2	K562	blood:
15	chr6:28804483..28808288-chr6:28953262..28955503,3	MCF-7	breast:
16	chr6:28802885..28808466-chr6:28831550..28836351,8	MCF-7	breast:
17	chr6:28802724..28808694-chr6:28856997..28865691,21	K562	blood:
18	chr6:28803772..28806116-chr6:28907591..28909225,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs13206458	0.91[EUR][1000 genomes]
rs13437309	0.86[AFR][1000 genomes]
rs3118357	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3118359	0.94[EUR][1000 genomes]
rs3118360	0.87[EUR][1000 genomes]
rs3118361	0.91[EUR][1000 genomes]
rs3118364	0.89[EUR][1000 genomes]
rs3118365	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3118366	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118367	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129791	0.83[EUR][1000 genomes]
rs3129794	0.91[EUR][1000 genomes]
rs3129797	0.91[EUR][1000 genomes]
rs3129798	0.91[EUR][1000 genomes]
rs3130837	0.94[EUR][1000 genomes]
rs3130838	0.94[EUR][1000 genomes]
rs3130844	0.91[EUR][1000 genomes]
rs3130845	0.91[EUR][1000 genomes]
rs3130846	0.87[EUR][1000 genomes]
rs3130847	0.91[EUR][1000 genomes]
rs3130885	0.89[EUR][1000 genomes]
rs3130887	0.92[EUR][1000 genomes]
rs3130888	0.91[EUR][1000 genomes]
rs3130890	0.80[EUR][1000 genomes]
rs3130891	0.91[EUR][1000 genomes]
rs3130892	0.91[EUR][1000 genomes]
rs3130893	0.91[EUR][1000 genomes]
rs3130894	0.91[EUR][1000 genomes]
rs3130895	0.89[EUR][1000 genomes]
rs3130896	0.91[EUR][1000 genomes]
rs3131068	0.91[EUR][1000 genomes]
rs3131069	0.91[EUR][1000 genomes]
rs3131071	0.91[EUR][1000 genomes]
rs3131072	0.91[EUR][1000 genomes]
rs3131073	0.87[EUR][1000 genomes]
rs3131075	0.91[EUR][1000 genomes]
rs3131076	0.91[EUR][1000 genomes]
rs3131081	0.91[EUR][1000 genomes]
rs3131093	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131094	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131095	0.94[EUR][1000 genomes]
rs3131096	0.94[EUR][1000 genomes]
rs3131097	0.94[EUR][1000 genomes]
rs3131101	0.94[EUR][1000 genomes]
rs3131335	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131336	0.94[EUR][1000 genomes]
rs3131340	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131341	0.83[EUR][1000 genomes]
rs3131343	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3131345	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132373	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3132374	0.91[EUR][1000 genomes]
rs3132376	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132378	0.94[EUR][1000 genomes]
rs3132382	0.91[EUR][1000 genomes]
rs3132384	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132385	0.94[EUR][1000 genomes]
rs3132387	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132388	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3132389	0.94[EUR][1000 genomes]
rs3132391	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132392	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3132393	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132394	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132395	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132396	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3135293	0.94[EUR][1000 genomes]
rs3135294	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3135295	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135298	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135299	0.90[EUR][1000 genomes]
rs3135300	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135302	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135304	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135306	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135307	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3135308	0.94[EUR][1000 genomes]
rs3135309	0.94[EUR][1000 genomes]
rs3135310	0.94[EUR][1000 genomes]
rs3135311	0.94[EUR][1000 genomes]
rs3135312	0.94[EUR][1000 genomes]
rs3135313	0.94[EUR][1000 genomes]
rs3135316	0.94[EUR][1000 genomes]
rs3135317	0.91[EUR][1000 genomes]
rs3135318	0.91[EUR][1000 genomes]
rs3135325	0.91[EUR][1000 genomes]
rs4324798	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6928657	0.81[AFR][1000 genomes]
rs7760313	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7761321	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7764642	0.86[AFR][1000 genomes]
rs7766699	0.84[AFR][1000 genomes]
rs7767099	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9257183	0.84[AFR][1000 genomes]
rs9257184	0.84[AFR][1000 genomes]
rs9257187	0.84[AFR][1000 genomes]
rs9257188	0.80[AFR][1000 genomes]
rs9257189	0.84[AFR][1000 genomes]
rs9257192	0.84[AFR][1000 genomes]
rs9257217	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9257223	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9257227	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257245	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9257249	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257250	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9257262	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257267	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9257272	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9257331	0.94[EUR][1000 genomes]
rs9257345	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3135297	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3135297	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3135297	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28802200-28805000	Weak transcription	K562	blood
2	chr6:28802400-28805200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:28804200-28807400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:28804400-28805000	Bivalent Enhancer	HepG2	liver

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