Variant report

Variant	rs9393986
Chromosome Location	chr6:29973526-29973527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:29973328-29973529	HepG2	liver:	n/a	n/a
2	CEBPB	chr6:29973309-29973602	IMR90	lung:	n/a	n/a
3	CEBPB	chr6:29973261-29973642	HepG2	liver:	n/a	n/a
4	HDAC2	chr6:29973283-29973706	HepG2	liver:	n/a	n/a
5	CEBPB	chr6:29973264-29973643	HepG2	liver:	n/a	n/a
6	SMC3	chr6:29973278-29973753	HepG2	liver:	n/a	n/a
7	RAD21	chr6:29973337-29973586	HepG2	liver:	n/a	n/a
8	CEBPB	chr6:29973276-29973599	HepG2	liver:	n/a	n/a
9	RAD21	chr6:29973291-29973598	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HLA-J	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10947050	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11752303	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12193100	0.84[EUR][1000 genomes]
rs12193110	0.81[EUR][1000 genomes]
rs12195207	0.85[EUR][1000 genomes]
rs12195260	0.86[EUR][1000 genomes]
rs12200084	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12202241	0.86[EUR][1000 genomes]
rs12206499	0.85[EUR][1000 genomes]
rs2071568	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2275855	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394247	0.80[EUR][1000 genomes]
rs2508035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2523935	0.81[EUR][1000 genomes]
rs33959627	0.96[AFR][1000 genomes]
rs35066870	0.87[EUR][1000 genomes]
rs35159526	0.87[EUR][1000 genomes]
rs3807031	0.96[AFR][1000 genomes]
rs3823352	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3823353	0.85[EUR][1000 genomes]
rs3823354	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3823355	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3823358	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3823369	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3910312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4248141	0.80[EUR][1000 genomes]
rs4248142	0.80[EUR][1000 genomes]
rs4248143	0.80[EUR][1000 genomes]
rs4711206	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711209	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713269	0.80[EUR][1000 genomes]
rs4713270	0.80[EUR][1000 genomes]
rs4713274	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713275	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4713279	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947244	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959010	0.88[EUR][1000 genomes]
rs4959038	0.80[EUR][1000 genomes]
rs4959039	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4959040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903753	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6904029	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6916422	0.85[EUR][1000 genomes]
rs6916451	0.85[EUR][1000 genomes]
rs6935024	0.80[EUR][1000 genomes]
rs7766469	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295825	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295826	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295830	0.93[AFR][1000 genomes]
rs9348835	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357088	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9357092	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366750	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9366752	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9378141	0.80[EUR][1000 genomes]
rs9378142	0.84[EUR][1000 genomes]
rs9380150	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393984	0.83[EUR][1000 genomes]
rs9393987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393988	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393989	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9405044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
9	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
13	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
14	nsv601475	chr6:29963179-29977973	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9393986	HLA-H	cis	lymphoblastoid	seeQTL
rs9393986	ZKSCAN3	cis	cerebellum	SCAN
rs9393986	HLA-A	cis	lymphoblastoid	seeQTL
rs9393986	HLA.A29.1	cis	multi-tissue	Pritchard
rs9393986	HLA-G	Cis_1M	lymphoblastoid	RTeQTL
rs9393986	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs9393986	HIST1H2AI	cis	parietal	SCAN
rs9393986	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9393986	HIST1H2AH	cis	cerebellum	SCAN
rs9393986	LOC730399///LOC731974	Cis_1M	lymphoblastoid	RTeQTL
rs9393986	BTN2A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29964400-29974400	Weak transcription	Hela-S3	cervix
2	chr6:29966800-29974000	Weak transcription	Spleen	Spleen
3	chr6:29970800-29973800	Weak transcription	Ovary	ovary
4	chr6:29971000-29973800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:29971000-29974000	Weak transcription	HMEC	breast
6	chr6:29973000-29973600	Enhancers	HepG2	liver
7	chr6:29973400-29973600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:29973400-29973800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
9	chr6:29973400-29973800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr6:29973400-29973800	Enhancers	Colon Smooth Muscle	Colon
11	chr6:29973400-29973800	Enhancers	Stomach Mucosa	stomach
12	chr6:29973400-29973800	Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links