Variant report

Variant	rs1284980
Chromosome Location	chr6:45081428-45081429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45071425..45074350-chr6:45080859..45082948,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1023089	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1041332	0.82[AMR][1000 genomes]
rs10948198	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11968042	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12190261	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12204678	0.85[ASN][1000 genomes]
rs12205071	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12208023	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12208339	0.81[EUR][1000 genomes]
rs12208483	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12529490	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1284961	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1284965	0.82[AMR][1000 genomes]
rs1284969	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1284972	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1284973	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1284975	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1284982	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1284983	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1284988	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1284992	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1285004	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1285013	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1285014	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1285019	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1285022	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1285023	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1285026	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1290386	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1300126	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1304168	0.82[AMR][1000 genomes]
rs13202529	0.82[AMR][1000 genomes]
rs13207575	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1324532	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1324537	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1324540	0.82[AMR][1000 genomes]
rs1329714	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1359336	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1411148	0.86[AMR][1000 genomes]
rs1581777	0.82[AMR][1000 genomes]
rs1629542	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1748231	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1748234	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1748235	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1748237	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1748242	0.84[AMR][1000 genomes]
rs1797145	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1797147	0.83[AMR][1000 genomes]
rs1886345	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1937046	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1937047	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1971482	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2186062	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35817842	0.85[AMR][1000 genomes]
rs3920903	0.86[AMR][1000 genomes]
rs4398713	0.82[AMR][1000 genomes]
rs4412189	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4714836	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56138724	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6458418	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6458419	0.89[ASN][1000 genomes]
rs6458420	0.86[ASN][1000 genomes]
rs6458425	0.80[ASN][1000 genomes]
rs6458430	0.82[AMR][1000 genomes]
rs6899378	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6901786	0.82[AMR][1000 genomes]
rs6905396	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6910974	0.86[AMR][1000 genomes]
rs6923436	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6925467	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6938316	0.82[AMR][1000 genomes]
rs7738526	0.80[ASN][1000 genomes]
rs7739928	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7743116	0.80[ASN][1000 genomes]
rs7750380	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7758031	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7763450	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7763973	0.86[AMR][1000 genomes]
rs7764102	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs927658	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9349309	0.84[AMR][1000 genomes]
rs9349313	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9349315	0.80[ASN][1000 genomes]
rs9357470	0.85[ASN][1000 genomes]
rs9367214	0.84[AMR][1000 genomes]
rs9369529	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9369534	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9381361	0.82[AMR][1000 genomes]
rs9381364	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9381365	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9381366	0.86[ASN][1000 genomes]
rs9395063	0.84[AMR][1000 genomes]
rs9395065	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395066	0.88[ASN][1000 genomes]
rs9472451	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs964452	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs969211	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs988147	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv603008	chr6:44958372-45081821	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	nsv528130	chr6:45056086-45083966	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	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
rs1284980	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45073400-45083600	Weak transcription	Pancreas	Pancrea
2	chr6:45076600-45082800	Weak transcription	Dnd41	blood
3	chr6:45077800-45083400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:45078400-45083400	Weak transcription	HSMM	muscle
5	chr6:45081200-45083200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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