Variant report

Variant	rs9399564
Chromosome Location	chr6:146078907-146078908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:146055254..146056868-chr6:146078510..146080192,2	K562	blood:
2	chr6:146055254..146057948-chr6:146078692..146080698,2	K562	blood:
3	chr6:146078233..146080576-chr6:146117352..146119241,2	K562	blood:
4	chr6:146071338..146074051-chr6:146075852..146079781,4	K562	blood:
5	chr6:146052881..146057901-chr6:146075302..146079376,6	MCF-7	breast:
6	chr6:146077264..146080093-chr6:146082462..146084742,2	K562	blood:
7	chr6:146054115..146058275-chr6:146075564..146080961,9	MCF-7	breast:
8	chr6:146077433..146080093-chr6:146081653..146083962,2	K562	blood:
9	chr6:146063820..146065547-chr6:146076992..146079128,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270638	Chromatin interaction
ENSG00000112425	Chromatin interaction

Extended variants
information (count: 215 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:214)

rs_ID	r²[population]
rs1004752	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1011596	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1011597	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214925	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10447449	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1045820	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1055212	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1062068	0.82[ASN][1000 genomes]
rs1070516	0.81[EUR][1000 genomes]
rs1070517	0.82[EUR][1000 genomes]
rs1070519	0.81[EUR][1000 genomes]
rs10872579	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10872580	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11155442	0.95[EUR][1000 genomes]
rs11965018	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12190966	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12199362	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12211884	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1292333	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1292334	0.84[EUR][1000 genomes]
rs1292336	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1292337	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1292338	0.81[EUR][1000 genomes]
rs13214277	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1337839	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1337840	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1337841	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13437042	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1415744	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1415746	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1415747	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1569540	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1577916	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1832362	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1883365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1890171	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935616	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1986729	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2050027	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064185	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072911	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2092262	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2092263	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2142981	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142983	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2179323	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2235482	0.80[EUR][1000 genomes]
rs2246334	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249147	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2249386	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253194	0.87[EUR][1000 genomes]
rs2253307	0.87[EUR][1000 genomes]
rs2253654	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2253764	0.85[EUR][1000 genomes]
rs2253768	0.86[EUR][1000 genomes]
rs2253880	0.85[EUR][1000 genomes]
rs2253886	0.85[EUR][1000 genomes]
rs2253887	0.83[EUR][1000 genomes]
rs2254257	0.82[ASN][1000 genomes]
rs2265474	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265915	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265916	0.92[EUR][1000 genomes]
rs2328704	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2328707	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2328709	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485632	0.89[EUR][1000 genomes]
rs2814879	0.85[EUR][1000 genomes]
rs371186	0.81[EUR][1000 genomes]
rs3811102	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs409553	0.81[EUR][1000 genomes]
rs426874	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4332001	0.80[EUR][1000 genomes]
rs439035	0.81[EUR][1000 genomes]
rs441290	0.81[EUR][1000 genomes]
rs4455694	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs446031	0.81[EUR][1000 genomes]
rs453834	0.81[EUR][1000 genomes]
rs4634475	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4895683	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4895684	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4896820	0.81[EUR][1000 genomes]
rs4896824	0.81[EUR][1000 genomes]
rs4896832	0.84[EUR][1000 genomes]
rs4896833	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4896837	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896838	0.89[EUR][1000 genomes]
rs4896839	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896841	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4896842	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4896843	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4896844	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55810423	0.87[EUR][1000 genomes]
rs57700188	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62433835	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62435810	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62438257	0.84[AMR][1000 genomes]
rs6570700	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6570701	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6570703	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6570705	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6570706	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6570708	0.80[EUR][1000 genomes]
rs6570713	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570716	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570717	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570719	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570723	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6570724	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6899900	0.81[EUR][1000 genomes]
rs6901888	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6902913	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6906258	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906402	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915718	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917135	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6919684	0.81[EUR][1000 genomes]
rs6921073	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6923678	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6928007	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930154	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6931553	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6932863	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6933161	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937661	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6941429	0.80[EUR][1000 genomes]
rs697053	0.80[EUR][1000 genomes]
rs697054	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs697055	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs697056	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs702304	0.81[EUR][1000 genomes]
rs702305	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs702306	0.81[EUR][1000 genomes]
rs702307	0.82[EUR][1000 genomes]
rs702309	0.80[EUR][1000 genomes]
rs702314	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs702317	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702318	0.89[EUR][1000 genomes]
rs702319	0.89[EUR][1000 genomes]
rs702320	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702321	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs702323	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs702324	0.89[EUR][1000 genomes]
rs735535	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs735536	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7739735	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7740785	0.82[EUR][1000 genomes]
rs7742333	0.91[EUR][1000 genomes]
rs7744014	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7745696	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7752286	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753770	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753833	0.83[EUR][1000 genomes]
rs7762536	0.80[EUR][1000 genomes]
rs7762562	0.92[EUR][1000 genomes]
rs7772717	0.80[EUR][1000 genomes]
rs7773939	0.81[EUR][1000 genomes]
rs857875	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs857877	0.84[EUR][1000 genomes]
rs857879	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs857880	0.84[EUR][1000 genomes]
rs857881	0.80[EUR][1000 genomes]
rs857882	0.84[EUR][1000 genomes]
rs857883	0.84[EUR][1000 genomes]
rs870491	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9373471	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9373473	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9373475	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9373476	0.95[EUR][1000 genomes]
rs9376954	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9376956	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9376957	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9376961	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9376968	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9386128	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9386131	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9386132	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386133	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9386134	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390343	0.82[EUR][1000 genomes]
rs9390344	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9390348	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9390349	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9390354	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9390355	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390356	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390357	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9390358	0.94[EUR][1000 genomes]
rs9399555	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9399559	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9399561	0.80[EUR][1000 genomes]
rs9399565	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9399567	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403737	0.84[EUR][1000 genomes]
rs9403739	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9403741	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9403742	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403746	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9403747	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9403749	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403750	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9485018	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9485019	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9485021	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9485024	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9497380	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9497395	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9497396	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9497398	0.83[EUR][1000 genomes]
rs9497401	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9497406	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9497419	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs952405	0.80[EUR][1000 genomes]
rs991507	0.87[EUR][1000 genomes];0.87[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	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399564	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146074400-146079200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:146077400-146079800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:146077800-146079000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:146078000-146079000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:146078000-146079200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:146078800-146079400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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