Variant report

Variant	rs2038766
Chromosome Location	chr6:45092212-45092213
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45092014..45095175-chr6:45095501..45098870,4	K562	blood:
2	chr6:45091825..45094517-chr6:45344694..45347186,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1023090	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12204678	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1284961	0.81[ASN][1000 genomes]
rs1284972	0.86[ASN][1000 genomes]
rs1284973	0.87[ASN][1000 genomes]
rs1284975	0.87[ASN][1000 genomes]
rs1284988	0.84[ASN][1000 genomes]
rs1284992	0.85[ASN][1000 genomes]
rs1285004	0.87[ASN][1000 genomes]
rs1285013	0.81[ASN][1000 genomes]
rs1285014	0.81[ASN][1000 genomes]
rs1285019	0.81[ASN][1000 genomes]
rs1285022	0.87[ASN][1000 genomes]
rs1285023	0.87[ASN][1000 genomes]
rs1285026	0.86[ASN][1000 genomes]
rs1290386	0.81[ASN][1000 genomes]
rs1300126	0.87[ASN][1000 genomes]
rs1324531	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1324532	0.85[ASN][1000 genomes]
rs1324537	0.86[ASN][1000 genomes]
rs1329713	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1359336	0.86[ASN][1000 genomes]
rs1555681	0.89[EUR][1000 genomes]
rs1886345	0.88[ASN][1000 genomes]
rs2093901	0.84[EUR][1000 genomes]
rs2093903	0.84[EUR][1000 genomes]
rs2396380	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2396425	0.83[EUR][1000 genomes]
rs6458419	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458420	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458425	0.81[ASN][1000 genomes]
rs6458428	0.83[EUR][1000 genomes]
rs6899378	0.87[ASN][1000 genomes]
rs6899845	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6905396	0.81[ASN][1000 genomes]
rs6933553	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7738526	0.81[ASN][1000 genomes]
rs7739928	0.83[ASN][1000 genomes]
rs7743116	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7750380	0.86[ASN][1000 genomes]
rs927658	0.81[ASN][1000 genomes]
rs9349313	0.87[ASN][1000 genomes]
rs9349315	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9357469	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9357470	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357471	0.91[EUR][1000 genomes]
rs9357478	0.84[EUR][1000 genomes]
rs9369533	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9369534	0.86[ASN][1000 genomes]
rs9381364	0.86[ASN][1000 genomes]
rs9381365	0.88[ASN][1000 genomes]
rs9381366	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9395065	0.85[ASN][1000 genomes]
rs9395066	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9395069	0.85[EUR][1000 genomes]
rs9395079	0.86[EUR][1000 genomes]
rs988147	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1026728	chr6:45001948-45126730	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538213	chr6:45001948-45126730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv885865	chr6:45012223-45102025	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1032906	chr6:45069368-45212863	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038766	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45089000-45099400	Weak transcription	Fetal Heart	heart
2	chr6:45092000-45092400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links