Variant report

Variant	rs6458428
Chromosome Location	chr6:45179815-45179816
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45160972..45165246-chr6:45178939..45182549,3	K562	blood:
2	chr6:45171517..45174411-chr6:45178235..45180217,2	K562	blood:
3	chr15:98568515..98569332-chr6:45179144..45180022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252477	Chromatin interaction

Extended variants
information (count: 232 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:225)

rs_ID	r²[population]
rs1041332	0.80[ASN][1000 genomes]
rs10456552	0.84[ASN][1000 genomes]
rs1080415	0.97[ASN][1000 genomes]
rs10807318	0.99[ASN][1000 genomes]
rs10807319	0.97[ASN][1000 genomes]
rs10807320	0.95[ASN][1000 genomes]
rs10948222	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10948229	0.86[ASN][1000 genomes]
rs11968042	0.87[ASN][1000 genomes]
rs12190261	0.81[ASN][1000 genomes]
rs12194311	0.84[ASN][1000 genomes]
rs12199720	0.86[ASN][1000 genomes]
rs12204678	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12205071	0.82[ASN][1000 genomes]
rs12205274	0.92[ASN][1000 genomes]
rs12205312	0.82[ASN][1000 genomes]
rs12208023	0.82[ASN][1000 genomes]
rs12208483	0.87[ASN][1000 genomes]
rs12208924	0.84[ASN][1000 genomes]
rs12524323	0.85[ASN][1000 genomes]
rs12526807	0.81[ASN][1000 genomes]
rs12527743	0.82[ASN][1000 genomes]
rs12529946	0.92[ASN][1000 genomes]
rs12662272	0.81[ASN][1000 genomes]
rs1284955	0.86[ASN][1000 genomes]
rs1284961	0.98[ASN][1000 genomes]
rs1284962	0.86[ASN][1000 genomes]
rs1284964	0.86[ASN][1000 genomes]
rs1284965	1.00[ASN][1000 genomes]
rs1284967	0.86[ASN][1000 genomes]
rs1284969	0.93[ASN][1000 genomes]
rs1284972	0.88[ASN][1000 genomes]
rs1284973	0.89[ASN][1000 genomes]
rs1284975	0.89[ASN][1000 genomes]
rs1284988	0.89[ASN][1000 genomes]
rs1284992	0.90[ASN][1000 genomes]
rs1284993	0.81[ASN][1000 genomes]
rs1285004	0.89[ASN][1000 genomes]
rs1285005	0.81[ASN][1000 genomes]
rs1285006	0.81[ASN][1000 genomes]
rs1285007	0.82[ASN][1000 genomes]
rs1285008	0.81[ASN][1000 genomes]
rs1285009	0.81[ASN][1000 genomes]
rs1285010	0.81[ASN][1000 genomes]
rs1285011	0.81[ASN][1000 genomes]
rs1285013	0.95[ASN][1000 genomes]
rs1285014	0.95[ASN][1000 genomes]
rs1285019	0.98[ASN][1000 genomes]
rs1285020	0.80[ASN][1000 genomes]
rs1285021	0.81[ASN][1000 genomes]
rs1285022	0.92[ASN][1000 genomes]
rs1285023	0.92[ASN][1000 genomes]
rs1285026	0.91[ASN][1000 genomes]
rs1285027	0.82[ASN][1000 genomes]
rs1285028	0.81[ASN][1000 genomes]
rs1285029	0.81[ASN][1000 genomes]
rs1285030	0.81[ASN][1000 genomes]
rs1285031	0.80[ASN][1000 genomes]
rs1285033	0.82[ASN][1000 genomes]
rs1290386	0.98[ASN][1000 genomes]
rs1300126	0.89[ASN][1000 genomes]
rs1304168	0.98[ASN][1000 genomes]
rs13207575	0.82[ASN][1000 genomes]
rs1324530	0.82[ASN][1000 genomes]
rs1324531	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1324532	0.87[ASN][1000 genomes]
rs1324535	0.81[ASN][1000 genomes]
rs1324537	0.91[ASN][1000 genomes]
rs1324540	0.96[ASN][1000 genomes]
rs1359336	0.91[ASN][1000 genomes]
rs1411148	0.88[ASN][1000 genomes]
rs1581777	0.97[ASN][1000 genomes]
rs1629542	0.93[ASN][1000 genomes]
rs16873257	0.86[ASN][1000 genomes]
rs17288278	0.86[ASN][1000 genomes]
rs1748231	0.93[ASN][1000 genomes]
rs1748233	0.81[ASN][1000 genomes]
rs1748234	0.93[ASN][1000 genomes]
rs1748235	0.93[ASN][1000 genomes]
rs1748236	0.81[ASN][1000 genomes]
rs1748237	0.88[ASN][1000 genomes]
rs1748238	0.82[ASN][1000 genomes]
rs1748240	0.81[ASN][1000 genomes]
rs1748242	0.93[ASN][1000 genomes]
rs1797145	0.93[ASN][1000 genomes]
rs1797147	0.92[ASN][1000 genomes]
rs1797156	0.81[ASN][1000 genomes]
rs1852986	0.85[ASN][1000 genomes]
rs1853652	0.81[ASN][1000 genomes]
rs1886345	0.90[ASN][1000 genomes]
rs1937046	0.87[ASN][1000 genomes]
rs1937047	0.87[ASN][1000 genomes]
rs2038766	0.83[EUR][1000 genomes]
rs2057552	0.82[ASN][1000 genomes]
rs2057553	0.82[ASN][1000 genomes]
rs2093901	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093903	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186062	0.82[ASN][1000 genomes]
rs2396380	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2396381	0.81[ASN][1000 genomes]
rs2396425	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396426	0.84[ASN][1000 genomes]
rs2396504	0.84[ASN][1000 genomes]
rs2763134	0.82[ASN][1000 genomes]
rs2815263	0.86[ASN][1000 genomes]
rs34167737	0.83[ASN][1000 genomes]
rs35817842	0.80[ASN][1000 genomes]
rs3920903	0.88[ASN][1000 genomes]
rs3923353	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072928	0.86[ASN][1000 genomes]
rs4352679	0.95[ASN][1000 genomes]
rs4373351	0.83[ASN][1000 genomes]
rs4412189	0.80[ASN][1000 genomes]
rs4446571	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4463250	0.80[ASN][1000 genomes]
rs4506035	0.82[EUR][1000 genomes]
rs4521586	0.81[ASN][1000 genomes]
rs4521587	0.81[ASN][1000 genomes]
rs4610549	0.82[ASN][1000 genomes]
rs4631280	0.80[EUR][1000 genomes]
rs4714836	0.82[ASN][1000 genomes]
rs4714842	0.86[ASN][1000 genomes]
rs4714845	0.95[ASN][1000 genomes]
rs4714846	0.83[ASN][1000 genomes]
rs4714847	0.97[ASN][1000 genomes]
rs4714848	0.97[ASN][1000 genomes]
rs56138724	0.88[ASN][1000 genomes]
rs56175185	0.82[ASN][1000 genomes]
rs6458418	0.81[ASN][1000 genomes]
rs6458419	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6458420	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458423	0.89[ASN][1000 genomes]
rs6458425	0.98[ASN][1000 genomes]
rs6458427	1.00[ASN][1000 genomes]
rs6458430	1.00[ASN][1000 genomes]
rs6458432	0.82[ASN][1000 genomes]
rs6458433	0.82[ASN][1000 genomes]
rs6458434	0.83[ASN][1000 genomes]
rs6458435	0.82[ASN][1000 genomes]
rs6458441	0.85[ASN][1000 genomes]
rs6899378	0.89[ASN][1000 genomes]
rs6899845	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6901161	0.82[ASN][1000 genomes]
rs6901786	1.00[ASN][1000 genomes]
rs6905396	0.98[ASN][1000 genomes]
rs6917352	0.84[ASN][1000 genomes]
rs6917594	0.81[ASN][1000 genomes]
rs6923436	0.87[ASN][1000 genomes]
rs6928753	0.84[ASN][1000 genomes]
rs6932804	0.84[ASN][1000 genomes]
rs6933449	0.84[ASN][1000 genomes]
rs6933553	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6934594	0.84[ASN][1000 genomes]
rs6935398	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6936475	0.81[ASN][1000 genomes]
rs6937317	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6938177	0.86[ASN][1000 genomes]
rs6938316	0.99[ASN][1000 genomes]
rs6941169	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73449282	0.81[ASN][1000 genomes]
rs73735337	0.82[ASN][1000 genomes]
rs73735338	0.81[ASN][1000 genomes]
rs7451423	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738526	0.98[ASN][1000 genomes]
rs7739928	0.88[ASN][1000 genomes]
rs7740083	0.86[ASN][1000 genomes]
rs7740542	0.82[ASN][1000 genomes]
rs7743116	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7750380	0.91[ASN][1000 genomes]
rs7757282	0.85[ASN][1000 genomes]
rs7758031	0.82[ASN][1000 genomes]
rs7763450	0.86[ASN][1000 genomes]
rs7763973	0.80[ASN][1000 genomes]
rs7767025	0.90[ASN][1000 genomes]
rs7769231	0.86[ASN][1000 genomes]
rs927658	0.98[ASN][1000 genomes]
rs9296452	0.83[ASN][1000 genomes]
rs9296453	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296455	0.95[ASN][1000 genomes]
rs9296457	0.83[ASN][1000 genomes]
rs9296458	0.86[ASN][1000 genomes]
rs9349309	0.82[ASN][1000 genomes]
rs9349313	0.92[ASN][1000 genomes]
rs9349315	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357469	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357470	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357471	0.80[EUR][1000 genomes]
rs9357478	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357480	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357484	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367214	0.82[ASN][1000 genomes]
rs9369530	0.82[ASN][1000 genomes]
rs9369533	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9369534	0.91[ASN][1000 genomes]
rs9369549	0.84[ASN][1000 genomes]
rs9369552	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9369558	0.86[ASN][1000 genomes]
rs9381361	0.80[ASN][1000 genomes]
rs9381364	0.91[ASN][1000 genomes]
rs9381365	0.90[ASN][1000 genomes]
rs9381366	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9381373	1.00[ASN][1000 genomes]
rs9381377	0.89[EUR][1000 genomes]
rs9381383	0.86[ASN][1000 genomes]
rs9395063	0.88[ASN][1000 genomes]
rs9395065	0.90[ASN][1000 genomes]
rs9395066	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9395069	0.83[EUR][1000 genomes]
rs9395079	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9395081	0.85[ASN][1000 genomes]
rs9395084	0.84[EUR][1000 genomes]
rs9395086	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395087	0.83[EUR][1000 genomes]
rs9395088	0.95[ASN][1000 genomes]
rs9395095	0.86[ASN][1000 genomes]
rs9463076	0.97[ASN][1000 genomes]
rs9463078	0.94[EUR][1000 genomes]
rs9463081	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9463083	0.86[ASN][1000 genomes]
rs9472442	0.81[ASN][1000 genomes]
rs9472451	0.97[ASN][1000 genomes]
rs9472453	0.83[ASN][1000 genomes]
rs964452	0.94[ASN][1000 genomes]
rs969211	0.82[ASN][1000 genomes]
rs988147	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	nsv1028068	chr6:45169010-45246577	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6458428	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45178200-45182200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:45179000-45180200	Weak transcription	Dnd41	blood
3	chr6:45179800-45181000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr6:45179800-45182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:45179800-45182600	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links