Variant report

Variant	rs1233604
Chromosome Location	chr6:28734676-28734677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28731767..28734753-chr6:28735144..28738101,4	K562	blood:
2	chr6:28731867..28735071-chr6:28750775..28753093,3	K562	blood:
3	chr6:28733597..28735281-chr6:28802392..28805024,2	K562	blood:
4	chr6:28733571..28736534-chr6:28751232..28752788,2	K562	blood:

Variant related genes	Relation type
ENSG00000235559	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1233579	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233580	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233581	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233583	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233593	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1238262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1311911	0.94[EUR][1000 genomes]
rs1311912	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1311913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13194504	0.84[EUR][1000 genomes]
rs13206458	0.80[EUR][1000 genomes]
rs13217472	0.89[EUR][1000 genomes]
rs1742743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3118357	0.84[EUR][1000 genomes]
rs3118359	0.84[EUR][1000 genomes]
rs3118360	0.84[EUR][1000 genomes]
rs3118361	0.80[EUR][1000 genomes]
rs3118366	0.82[EUR][1000 genomes]
rs3118367	0.84[EUR][1000 genomes]
rs3130838	0.84[EUR][1000 genomes]
rs3130892	0.80[EUR][1000 genomes]
rs3131068	0.80[EUR][1000 genomes]
rs3131069	0.80[EUR][1000 genomes]
rs3131071	0.80[EUR][1000 genomes]
rs3131093	0.82[EUR][1000 genomes]
rs3131094	0.84[EUR][1000 genomes]
rs3131095	0.84[EUR][1000 genomes]
rs3131096	0.84[EUR][1000 genomes]
rs3131097	0.84[EUR][1000 genomes]
rs3131335	0.82[EUR][1000 genomes]
rs3131336	0.84[EUR][1000 genomes]
rs3131340	0.87[EUR][1000 genomes]
rs3131341	0.87[EUR][1000 genomes]
rs3131343	0.89[EUR][1000 genomes]
rs3131345	0.84[EUR][1000 genomes]
rs3132373	0.89[EUR][1000 genomes]
rs3132374	0.80[EUR][1000 genomes]
rs3132376	0.84[EUR][1000 genomes]
rs3132382	0.80[EUR][1000 genomes]
rs3132384	0.84[EUR][1000 genomes]
rs3132385	0.84[EUR][1000 genomes]
rs3132387	0.82[EUR][1000 genomes]
rs3132388	0.84[EUR][1000 genomes]
rs3132389	0.84[EUR][1000 genomes]
rs3132391	0.84[EUR][1000 genomes]
rs3132392	0.84[EUR][1000 genomes]
rs3132393	0.82[EUR][1000 genomes]
rs3132394	0.82[EUR][1000 genomes]
rs3132395	0.82[EUR][1000 genomes]
rs3132396	0.87[EUR][1000 genomes]
rs3135293	0.84[EUR][1000 genomes]
rs3135294	0.85[EUR][1000 genomes]
rs3135295	0.84[EUR][1000 genomes]
rs3135298	0.82[EUR][1000 genomes]
rs3135300	0.84[EUR][1000 genomes]
rs3135302	0.84[EUR][1000 genomes]
rs3135304	0.84[EUR][1000 genomes]
rs3135306	0.84[EUR][1000 genomes]
rs3135307	0.84[EUR][1000 genomes]
rs3135308	0.84[EUR][1000 genomes]
rs3135309	0.84[EUR][1000 genomes]
rs3135310	0.84[EUR][1000 genomes]
rs3135311	0.84[EUR][1000 genomes]
rs3135312	0.84[EUR][1000 genomes]
rs3135313	0.84[EUR][1000 genomes]
rs3135316	0.84[EUR][1000 genomes]
rs3135318	0.80[EUR][1000 genomes]
rs34724414	0.84[EUR][1000 genomes]
rs35044849	0.84[EUR][1000 genomes]
rs35243068	0.89[EUR][1000 genomes]
rs4324798	0.87[EUR][1000 genomes]
rs6456835	0.91[EUR][1000 genomes]
rs6908726	0.87[EUR][1000 genomes]
rs7760313	0.82[EUR][1000 genomes]
rs7761321	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7764642	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7766699	0.86[EUR][1000 genomes]
rs7767099	0.89[EUR][1000 genomes]
rs9257133	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257136	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257140	0.96[EUR][1000 genomes]
rs9257167	1.00[EUR][1000 genomes]
rs9257183	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257184	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257187	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257188	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257189	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257192	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257217	0.89[EUR][1000 genomes]
rs9257223	0.87[EUR][1000 genomes]
rs9257227	0.84[EUR][1000 genomes]
rs9257245	0.82[EUR][1000 genomes]
rs9257262	0.84[EUR][1000 genomes]
rs9257267	0.80[EUR][1000 genomes]
rs9257272	0.84[EUR][1000 genomes]
rs9257331	0.84[EUR][1000 genomes]
rs9393926	0.87[EUR][1000 genomes]
rs9393929	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1233604	BTN3A2	trans	lymphoblastoid	seeQTL
rs1233604	HLA-C	cis	multi-tissue	Pritchard
rs1233604	HLA-A	cis	multi-tissue	Pritchard
rs1233604	HLA-G	cis	multi-tissue	Pritchard
rs1233604	HLA-H	cis	multi-tissue	Pritchard
rs1233604	ZFP57	cis	multi-tissue	Pritchard
rs1233604	BTN3A2	cis	multi-tissue	Pritchard
rs1233604	ZFP57	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28733600-28740800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:28733800-28735000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr6:28734200-28735400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
4	chr6:28734400-28734800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
5	chr6:28734400-28734800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr6:28734400-28734800	Weak transcription	K562	blood
7	chr6:28734400-28735400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:28734400-28735600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr6:28734600-28734800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr6:28734600-28735000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:28734600-28735400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr6:28734600-28735400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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