Variant report

Variant	rs298029
Chromosome Location	chr5:58939500-58939501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58938220..58940371-chr5:58941651..58943411,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs159194	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs159196	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs159197	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs177077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs177078	0.83[ASN][1000 genomes]
rs294478	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs294479	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294481	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294482	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294483	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs294484	1.00[CHB][hapmap]
rs294485	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs294486	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs294492	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294494	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs294496	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294497	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294498	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs294500	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295943	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295944	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295946	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs295950	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295952	0.92[CHB][hapmap]
rs295953	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295954	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295955	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs295956	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs295963	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295964	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295966	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs295967	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295968	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295970	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295973	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs295979	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295980	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298014	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs298018	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs298025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298031	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298032	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298033	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs298034	0.92[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs298036	0.83[ASN][1000 genomes]
rs298038	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs298039	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs298040	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs298041	0.83[ASN][1000 genomes]
rs298043	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298044	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs298045	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs298046	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs298047	0.83[ASN][1000 genomes]
rs298048	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298051	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298052	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs37569	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs37571	1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv598256	chr5:58893286-58939840	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598257	chr5:58905769-58946639	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv462190	chr5:58936943-59023870	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv598258	chr5:58936943-59023870	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs298029	RAB3C	cis	cerebellum	SCAN
rs298029	MIER3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58923600-58957200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:58923800-58945000	Weak transcription	Aorta	Aorta
3	chr5:58927000-58939800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:58934800-58943800	Weak transcription	HUVEC	blood vessel
5	chr5:58936600-58949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:58937400-58940200	Weak transcription	Hela-S3	cervix
7	chr5:58937400-58940800	Weak transcription	A549	lung
8	chr5:58938800-58940000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:58938800-58940800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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