Variant report

Variant	rs2024970
Chromosome Location	chr6:26497520-26497521
allele	A/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	chr6:26497348-26497583	A549	lung:	n/a	chr6:26497460-26497471
2	CEBPB	chr6:26497385-26497585	IMR90	lung:	n/a	chr6:26497460-26497471
3	CEBPB	chr6:26497301-26497605	K562	blood:	n/a	chr6:26497460-26497471
4	CEBPB	chr6:26497315-26497573	HepG2	liver:	n/a	chr6:26497460-26497471

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26493704..26495272-chr6:26496094..26498091,2	K562	blood:
2	chr6:26497158..26499962-chr6:26521069..26523993,2	K562	blood:

Variant related genes	Relation type
BTN1A1	TF binding region
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1056347	0.82[EUR][1000 genomes]
rs1056667	0.82[EUR][1000 genomes]
rs1056668	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10946834	0.83[EUR][1000 genomes]
rs10946835	0.83[EUR][1000 genomes]
rs11754138	0.83[EUR][1000 genomes]
rs11756120	0.82[EUR][1000 genomes]
rs12525684	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12526680	0.81[CEU][hapmap]
rs1321479	0.85[EUR][1000 genomes]
rs1321480	0.83[EUR][1000 genomes]
rs1407045	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1535276	0.83[EUR][1000 genomes]
rs1614887	0.82[CEU][hapmap]
rs1624440	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs1796520	0.93[CEU][hapmap];0.84[CHB][hapmap];0.90[YRI][hapmap]
rs1796521	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs1977198	0.86[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2145318	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2208331	0.84[EUR][1000 genomes]
rs2255070	0.85[EUR][1000 genomes]
rs2393669	0.82[EUR][1000 genomes]
rs35355150	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3734540	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736781	0.85[EUR][1000 genomes]
rs3736782	0.85[EUR][1000 genomes]
rs3757151	0.83[EUR][1000 genomes]
rs4573	0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs4713006	0.83[EUR][1000 genomes]
rs4713008	0.82[CEU][hapmap]
rs6903973	0.85[EUR][1000 genomes]
rs6910899	0.83[EUR][1000 genomes]
rs6910930	0.83[EUR][1000 genomes]
rs6924865	0.82[EUR][1000 genomes]
rs6925703	0.83[EUR][1000 genomes]
rs6926629	0.85[EUR][1000 genomes]
rs71544291	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs742090	0.93[CEU][hapmap];0.84[CHB][hapmap];0.90[YRI][hapmap]
rs7763910	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs9295689	0.96[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs9295694	0.82[EUR][1000 genomes]
rs9295695	0.83[EUR][1000 genomes]
rs9357010	0.83[EUR][1000 genomes]
rs9358954	0.83[EUR][1000 genomes]
rs9379887	0.84[EUR][1000 genomes]
rs9393729	0.82[EUR][1000 genomes]
rs9393731	0.83[EUR][1000 genomes]
rs9393732	0.83[EUR][1000 genomes]
rs9461259	0.85[EUR][1000 genomes]
rs9461267	0.83[EUR][1000 genomes]
rs9467773	0.83[EUR][1000 genomes]
rs9467774	0.85[EUR][1000 genomes]
rs9467775	0.82[EUR][1000 genomes]
rs9467776	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2024970	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs2024970	HCG11	cis	normal skin	skin_eQTL
rs2024970	HCG11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26491600-26501600	Weak transcription	GM12878-XiMat	blood
2	chr6:26493600-26500400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:26494400-26497600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:26494800-26497600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:26497200-26498000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr6:26497200-26498200	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:26497400-26497600	Enhancers	Thymus	Thymus
8	chr6:26497400-26498200	Enhancers	K562	blood

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