Variant report

Variant	rs28415299
Chromosome Location	chr8:66548247-66548248
allele	G/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	MYC	chr8:66547983-66548282	NB4	blood:	n/a	n/a
2	MAX	chr8:66548087-66548285	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:66546894..66548678-chr8:66628274..66630820,2	MCF-7	breast:
2	chr8:66544222..66547080-chr8:66547679..66550589,3	MCF-7	breast:
3	chr8:66543941..66549000-chr8:66554498..66559366,10	MCF-7	breast:

Variant related genes	Relation type
ARMC1	TF binding region
ENSG00000066855	Chromatin interaction
ENSG00000104442	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10087361	0.95[ASN][1000 genomes]
rs10089029	0.95[ASN][1000 genomes]
rs10089708	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10092109	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10097461	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10100131	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1053085	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1053087	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1053088	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957361	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11776709	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11776712	0.89[ASN][1000 genomes]
rs11985628	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11990855	0.95[ASN][1000 genomes]
rs12335006	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12335276	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12543053	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12544767	0.91[ASN][1000 genomes]
rs12677419	0.93[ASN][1000 genomes]
rs12678467	0.94[ASN][1000 genomes]
rs13252358	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13266834	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13267942	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13281155	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs14213	0.94[ASN][1000 genomes]
rs1473601	0.95[ASN][1000 genomes]
rs1533285	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16932245	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16932250	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16932314	0.89[ASN][1000 genomes]
rs1877638	0.91[ASN][1000 genomes]
rs2048650	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2102648	0.93[ASN][1000 genomes]
rs2175809	0.93[ASN][1000 genomes]
rs2175810	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2357476	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28576524	0.93[ASN][1000 genomes]
rs28613797	0.95[ASN][1000 genomes]
rs3268	0.95[ASN][1000 genomes]
rs34226237	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34494846	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34533611	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34851482	0.95[ASN][1000 genomes]
rs35038843	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35790435	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35941313	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3750184	0.95[ASN][1000 genomes]
rs3765205	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812412	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4275254	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4320587	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4384017	0.81[ASN][1000 genomes]
rs4388482	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4397444	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4637885	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4637886	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737222	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4737747	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737748	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737749	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737750	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5018458	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57419568	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60023200	0.89[ASN][1000 genomes]
rs60058315	0.95[ASN][1000 genomes]
rs6472213	0.95[ASN][1000 genomes]
rs6472214	0.83[ASN][1000 genomes]
rs6472215	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6472216	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6472217	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6472218	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66467166	0.82[ASN][1000 genomes]
rs66486920	0.89[ASN][1000 genomes]
rs67046768	0.89[ASN][1000 genomes]
rs67131486	0.91[ASN][1000 genomes]
rs67685675	0.89[ASN][1000 genomes]
rs6985897	0.85[ASN][1000 genomes]
rs6985932	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986691	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986866	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6991731	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6993876	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6994213	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6995242	0.95[ASN][1000 genomes]
rs6997959	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7006261	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7006648	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7007505	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7012578	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7012856	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7016472	0.95[ASN][1000 genomes]
rs71930161	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73236948	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73236986	0.95[ASN][1000 genomes]
rs73239011	0.95[ASN][1000 genomes]
rs73239085	0.95[ASN][1000 genomes]
rs7459737	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7464123	0.89[ASN][1000 genomes]
rs7464223	0.92[ASN][1000 genomes]
rs7812390	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7812446	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7814841	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7815488	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7817112	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7823840	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7832407	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7835313	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7836349	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7836746	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7841652	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7842162	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7846527	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761434	chr8:65578467-66567678	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28415299	CTD-3025N20.3	cis	Muscle Skeletal	GTEx
rs28415299	CTD-3025N20.3	cis	lung	GTEx
rs28415299	CTD-3025N20.3	cis	Thyroid	GTEx
rs28415299	CTD-3025N20.3	cis	Artery Tibial	GTEx
rs28415299	CTD-3025N20.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66545600-66549400	Active TSS	A549	lung
2	chr8:66546400-66556000	Weak transcription	Small Intestine	intestine
3	chr8:66547000-66555800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr8:66547400-66556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:66547600-66548600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:66547600-66548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:66547600-66548600	Weak transcription	Hela-S3	cervix
8	chr8:66547600-66548600	Weak transcription	HMEC	breast
9	chr8:66547600-66548600	Weak transcription	NHEK	skin
10	chr8:66547600-66549000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr8:66547600-66549000	Weak transcription	NH-A	brain
12	chr8:66547600-66549200	Weak transcription	Osteobl	bone
13	chr8:66547600-66549800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr8:66547800-66548800	Active TSS	Placenta	Placenta
15	chr8:66547800-66549000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr8:66547800-66555200	Weak transcription	Pancreas	Pancrea
17	chr8:66548000-66549000	Weak transcription	HepG2	liver

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