Variant report

Variant	rs1542322
Chromosome Location	chr7:47772086-47772087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf69-3	chr7:47771952-47772894	ucscGeneNc_uc003tnx_2

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12374833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881580	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17172895	0.83[ASN][1000 genomes]
rs17172896	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17172897	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17172898	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17544941	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17627420	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55683481	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55745922	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56017135	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56024530	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57720210	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59963947	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60404365	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73093024	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093028	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093030	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093036	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093039	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093041	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093043	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093044	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093048	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093062	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093065	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094761	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73094779	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73094780	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73094782	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73094784	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73102790	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73102792	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73102794	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73102797	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73102799	0.85[EUR][1000 genomes]
rs73104703	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73104705	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73104711	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73104712	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73104714	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73104717	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73104718	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789757	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7790043	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7795201	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805780	0.83[ASN][1000 genomes]
rs7808100	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1018608	chr7:47708525-47831535	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1022906	chr7:47709936-47831535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015163	chr7:47734913-47832389	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv538831	chr7:47734913-47832389	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv522585	chr7:47764737-47777685	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv830990	chr7:47767540-47837584	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1542322	BLVRA	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47766000-47777400	Weak transcription	Spleen	Spleen
2	chr7:47766600-47772800	Weak transcription	Liver	Liver
3	chr7:47767000-47773800	Weak transcription	Fetal Kidney	kidney
4	chr7:47768600-47773800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:47770400-47772800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:47770400-47773600	Weak transcription	A549	lung
7	chr7:47770800-47774200	Enhancers	HepG2	liver
8	chr7:47771800-47773000	Enhancers	Primary B cells from peripheral blood	blood
9	chr7:47771800-47774400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:47772000-47773600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links