Variant report

Variant	rs2286404
Chromosome Location	chr6:29973620-29973621
allele	A/G
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	chr6:29973261-29973642	HepG2	liver:	n/a	n/a
2	HDAC2	chr6:29973283-29973706	HepG2	liver:	n/a	n/a
3	CEBPB	chr6:29973264-29973643	HepG2	liver:	n/a	n/a
4	SMC3	chr6:29973278-29973753	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HLA-J	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10484549	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896044	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16896923	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896970	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17179992	1.00[AFR][1000 genomes]
rs17180093	1.00[AFR][1000 genomes]
rs17180107	1.00[AFR][1000 genomes]
rs17180227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17180836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17186566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17187693	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17193696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17194467	1.00[AFR][1000 genomes]
rs2275854	0.84[ASN][1000 genomes]
rs2394249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2893999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3823368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3869062	1.00[AFR][1000 genomes]
rs4087724	1.00[AFR][1000 genomes]
rs4087726	1.00[AFR][1000 genomes]
rs41540614	1.00[AFR][1000 genomes]
rs41545022	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs41545117	1.00[AFR][1000 genomes]
rs41547618	1.00[AFR][1000 genomes]
rs41562213	1.00[AFR][1000 genomes]
rs55664658	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55808509	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55897388	1.00[AFR][1000 genomes]
rs55901207	1.00[AFR][1000 genomes]
rs55975201	1.00[AFR][1000 genomes]
rs56052321	1.00[AFR][1000 genomes]
rs56073777	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56147022	1.00[AFR][1000 genomes]
rs56149225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56171155	1.00[AFR][1000 genomes]
rs56181708	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56185319	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232426	1.00[AFR][1000 genomes]
rs56270681	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56289102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56369124	1.00[AFR][1000 genomes]
rs56378970	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58161072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58309428	1.00[AFR][1000 genomes]
rs61180635	1.00[AFR][1000 genomes]
rs62388660	1.00[AFR][1000 genomes]
rs62388661	1.00[AFR][1000 genomes]
rs62388723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62388749	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388750	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388751	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388752	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388754	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388755	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388756	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388757	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388764	1.00[AFR][1000 genomes]
rs62388798	1.00[AFR][1000 genomes]
rs62388799	1.00[AFR][1000 genomes]
rs62388801	1.00[AFR][1000 genomes]
rs62388802	1.00[AFR][1000 genomes]
rs62390160	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390162	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390181	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390402	1.00[AFR][1000 genomes]
rs62390510	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62390517	1.00[AFR][1000 genomes]
rs62390553	1.00[AFR][1000 genomes]
rs62390555	1.00[AFR][1000 genomes]
rs62392214	1.00[AFR][1000 genomes]
rs62392216	1.00[AFR][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

No data

Chromatin state (count:14 , 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	chr6:29973400-29973800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr6:29973400-29973800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:29973400-29973800	Enhancers	Colon Smooth Muscle	Colon
9	chr6:29973400-29973800	Enhancers	Stomach Mucosa	stomach
10	chr6:29973400-29973800	Active TSS	Stomach Smooth Muscle	stomach
11	chr6:29973600-29973800	Enhancers	Brain Hippocampus Middle	brain
12	chr6:29973600-29974000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:29973600-29974400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:29973600-29974400	Flanking Active TSS	HepG2	liver

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