Variant report

Variant	rs842805
Chromosome Location	chr1:192919372-192919373
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	chr1:192919060..192920783-chr1:192924059..192926249,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TROVE2-3	chr1:192917908-192919553	NONHSAT008553

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10754036	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801165	0.82[EUR][1000 genomes]
rs10801170	1.00[GIH][hapmap]
rs10921296	0.89[AMR][1000 genomes]
rs10921298	0.89[AMR][1000 genomes]
rs10921300	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12117621	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12118267	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12123511	1.00[GIH][hapmap]
rs12124274	0.97[EUR][1000 genomes]
rs12125252	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12132131	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12132305	1.00[GIH][hapmap]
rs12133193	0.89[EUR][1000 genomes]
rs12133295	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12138298	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143913	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1339591	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1339593	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1615218	0.89[AMR][1000 genomes]
rs17525308	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17592121	1.00[GIH][hapmap]
rs1769054	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2066216	0.81[EUR][1000 genomes]
rs2486496	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2487289	0.93[YRI][hapmap]
rs28461227	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2887640	1.00[GIH][hapmap]
rs35686688	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6428143	0.89[AMR][1000 genomes]
rs6680068	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6700102	0.82[AMR][1000 genomes]
rs6700111	0.82[AMR][1000 genomes]
rs710140	0.82[EUR][1000 genomes]
rs710141	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72738564	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738565	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738572	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72738574	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7415619	0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7512163	0.89[AMR][1000 genomes]
rs7512241	0.89[AMR][1000 genomes]
rs7513985	0.89[AMR][1000 genomes]
rs7547423	0.89[AMR][1000 genomes]
rs842792	0.82[EUR][1000 genomes]
rs842793	0.82[EUR][1000 genomes]
rs842794	0.82[EUR][1000 genomes]
rs842798	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs842799	0.93[YRI][hapmap]
rs842800	0.93[YRI][hapmap]
rs842801	0.93[YRI][hapmap]
rs842802	0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs842803	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs842806	0.93[YRI][hapmap]
rs842808	0.93[YRI][hapmap]
rs842811	0.93[YRI][hapmap]
rs842812	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs842815	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs844528	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9427824	0.89[AMR][1000 genomes]
rs9427825	0.89[AMR][1000 genomes]
rs946557	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs842805	GLRX2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192902000-192920800	Weak transcription	Aorta	Aorta
2	chr1:192908800-192921000	Weak transcription	NHEK	skin
3	chr1:192909000-192936600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:192912200-192921000	Weak transcription	HSMM	muscle
5	chr1:192915200-192920400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:192915200-192920600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:192917600-192927800	Weak transcription	Left Ventricle	heart

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