Variant report

Variant	rs1284966
Chromosome Location	chr6:45179587-45179588
allele	C/T
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: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10948230	0.80[ASN][1000 genomes]
rs12526462	0.80[ASN][1000 genomes]
rs12526649	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12526807	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12527743	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12529907	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12529990	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12530207	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12660412	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12662272	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12663469	0.80[ASN][1000 genomes]
rs1284955	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1284962	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1284964	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1284967	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1284979	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1284989	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1284993	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1284995	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1284999	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1285000	0.81[ASN][1000 genomes]
rs1285003	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1285005	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285006	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285007	0.87[ASN][1000 genomes]
rs1285008	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285009	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285010	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285011	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285020	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1285021	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285025	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1285027	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1285028	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285029	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285030	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1285031	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1285033	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1324530	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1324535	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1406848	0.80[ASN][1000 genomes]
rs16873257	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16873348	0.80[ASN][1000 genomes]
rs16873364	0.81[ASN][1000 genomes]
rs16873366	0.81[ASN][1000 genomes]
rs16873373	0.80[ASN][1000 genomes]
rs16873379	0.80[ASN][1000 genomes]
rs1748233	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1748236	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1748238	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1748240	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1797148	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1797149	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1797156	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1797159	0.80[ASN][1000 genomes]
rs1852985	0.81[ASN][1000 genomes]
rs1853652	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2024786	0.80[ASN][1000 genomes]
rs2057552	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2057553	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2295295	0.80[ASN][1000 genomes]
rs2295296	0.80[ASN][1000 genomes]
rs2396381	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2396426	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2763134	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2815263	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34167737	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34251367	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35134594	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35811020	0.80[ASN][1000 genomes]
rs4339452	0.84[ASN][1000 genomes]
rs4441951	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4521586	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4521587	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4711814	0.81[ASN][1000 genomes]
rs4714838	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4714842	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4714846	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55959525	0.84[ASN][1000 genomes]
rs56175185	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6458429	0.81[ASN][1000 genomes]
rs6458432	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6458433	0.90[ASN][1000 genomes]
rs6458434	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6458435	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6901161	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6905959	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6917352	0.92[ASN][1000 genomes]
rs6917594	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6926638	0.80[ASN][1000 genomes]
rs6932926	0.81[ASN][1000 genomes]
rs6936475	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6938592	0.86[ASN][1000 genomes]
rs6940983	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6941169	0.81[ASN][1000 genomes]
rs73449282	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73735337	0.87[ASN][1000 genomes]
rs73735338	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7740542	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7745506	0.82[ASN][1000 genomes]
rs9296452	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9369549	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9395081	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9463069	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9463070	0.80[ASN][1000 genomes]
rs9472442	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9472453	0.82[AMR][1000 genomes];0.89[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
rs1284966	SUPT3H	cis	brain	BrainEAC

Chromatin state (count:2 , 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

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