Variant report

Variant	rs6453494
Chromosome Location	chr5:79260219-79260220
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	chr5:79254651..79257793-chr5:79258388..79261777,3	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10035728	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10041212	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10041404	0.82[EUR][1000 genomes]
rs10043116	0.93[EUR][1000 genomes]
rs10060444	0.95[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs10062607	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs10064975	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs10065778	0.83[EUR][1000 genomes]
rs10066471	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10071601	0.92[EUR][1000 genomes]
rs10077238	0.93[EUR][1000 genomes]
rs1017996	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1017997	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1017998	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1032342	0.86[TSI][hapmap]
rs11741143	0.95[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11748289	0.92[EUR][1000 genomes]
rs13354864	0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1370987	0.95[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1438739	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs16877389	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2291524	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2404708	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2451929	0.94[EUR][1000 genomes]
rs2451930	0.81[EUR][1000 genomes]
rs2471105	0.86[TSI][hapmap]
rs2471106	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2471107	0.82[EUR][1000 genomes]
rs2471108	0.81[EUR][1000 genomes]
rs2471109	0.94[EUR][1000 genomes]
rs405878	0.93[EUR][1000 genomes]
rs422690	0.93[EUR][1000 genomes]
rs6453495	0.95[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6453496	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs6453497	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs6860568	0.83[EUR][1000 genomes]
rs6865678	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6868916	0.94[EUR][1000 genomes]
rs6870377	0.95[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs6873684	0.93[EUR][1000 genomes]
rs6882768	0.93[EUR][1000 genomes]
rs6887873	0.93[EUR][1000 genomes]
rs6892826	0.92[EUR][1000 genomes]
rs7446065	0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7734858	0.92[EUR][1000 genomes]
rs923636	0.86[TSI][hapmap]
rs9293795	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs963423	0.81[EUR][1000 genomes]
rs963424	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021113	chr5:79034662-79289828	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1822393	chr5:79195538-79260489	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6453494	CA2	trans	lymphoblastoid	seeQTL
rs6453494	THBS4	cis	cerebellum	SCAN
rs6453494	MTX3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79258800-79262400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:79259000-79260400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:79259000-79260600	Weak transcription	Fetal Brain Male	brain
4	chr5:79259200-79270800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:79259400-79269200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:79259400-79271400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:79259400-79272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:79259800-79260400	Enhancers	NHLF	lung
9	chr5:79260000-79263400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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