Variant report

Variant	rs66535980
Chromosome Location	chr2:64265970-64265971
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	chr2:64245315..64247719-chr2:64265223..64268057,2	MCF-7	breast:
2	chr2:64253837..64255979-chr2:64263941..64266708,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS54-3	chr2:64265716-64266380	NONHSAT071084
2	lnc-VPS54-3	chr2:64265719-64266380	refGeneNc_4218_NR_033837

Variant related genes	Relation type
ENSG00000143952	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10190776	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12463827	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12466966	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475294	0.87[EUR][1000 genomes]
rs12988017	0.81[EUR][1000 genomes]
rs12990604	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12993544	0.85[EUR][1000 genomes]
rs12996147	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997303	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12999675	0.87[EUR][1000 genomes]
rs13005218	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13007342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009774	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13010817	0.83[EUR][1000 genomes]
rs13014781	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015703	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13023542	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13025640	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13028805	0.82[EUR][1000 genomes]
rs13034260	0.87[EUR][1000 genomes]
rs1345479	0.87[EUR][1000 genomes]
rs1437455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545196	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17555655	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17562312	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17620012	0.87[EUR][1000 genomes]
rs17701685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17701709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002443	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287361	0.87[EUR][1000 genomes]
rs2422110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422111	0.86[AMR][1000 genomes]
rs34043307	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34145077	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34200806	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34239752	0.81[EUR][1000 genomes]
rs34512058	0.87[EUR][1000 genomes]
rs34683043	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34700615	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35058898	0.81[EUR][1000 genomes]
rs35122209	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35247801	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35521527	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35552326	0.80[EUR][1000 genomes]
rs35648996	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35693031	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35810427	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35939512	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35972278	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35975566	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36099158	0.81[EUR][1000 genomes]
rs3815616	0.87[EUR][1000 genomes]
rs3934536	0.85[EUR][1000 genomes]
rs4482470	0.87[EUR][1000 genomes]
rs4485552	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4544421	0.87[EUR][1000 genomes]
rs4599090	0.87[EUR][1000 genomes]
rs4671072	0.83[EUR][1000 genomes]
rs4671537	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671538	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671540	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671541	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66476638	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66595136	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66650505	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66660401	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66993685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67366434	0.82[EUR][1000 genomes]
rs6759803	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67962955	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71422402	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808231	0.87[EUR][1000 genomes]
rs72808248	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808254	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808262	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808287	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808296	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs874695	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs893779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64251200-64273200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:64261200-64266200	Weak transcription	HepG2	liver
3	chr2:64263600-64266800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:64263800-64266400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:64263800-64267400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:64263800-64267600	Weak transcription	HMEC	breast
7	chr2:64264000-64266200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:64264000-64267000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:64264000-64267000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:64264000-64267000	Weak transcription	Dnd41	blood
11	chr2:64264000-64267000	Weak transcription	HUVEC	blood vessel
12	chr2:64264000-64267400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:64264000-64267600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:64264200-64266600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:64264200-64266800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:64264400-64266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:64264400-64266600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:64264400-64266600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:64264400-64266600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:64264400-64266800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:64264400-64266800	Weak transcription	Fetal Thymus	thymus
22	chr2:64264800-64266000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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