Variant report

Variant	rs842789
Chromosome Location	chr1:192927694-192927695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TROVE2-3	chr1:192926858-192930165	NONHSAT008549

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1339589	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1339592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1578163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1612628	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1618583	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1769068	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769070	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1769071	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1770923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2486494	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2486495	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2486498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2487283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2487289	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59189492	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6661948	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6687899	1.00[MEX][hapmap]
rs73068182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73068192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7522932	1.00[MEX][hapmap]
rs7546076	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7553594	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7553830	1.00[MEX][hapmap]
rs842784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842785	0.81[AFR][1000 genomes]
rs842786	0.81[AFR][1000 genomes]
rs842787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842788	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842799	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842800	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842801	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842805	0.86[YRI][hapmap]
rs842806	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842808	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842811	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs842813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs863600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs866381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946556	1.00[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192909000-192936600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:192917600-192927800	Weak transcription	Left Ventricle	heart
3	chr1:192922200-192928000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:192922200-192928000	Weak transcription	HSMM	muscle
5	chr1:192922400-192927800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:192922400-192927800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:192922400-192941000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:192923400-192931600	Weak transcription	Primary T cells from cord blood	blood
9	chr1:192925200-192928800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:192925400-192927800	Weak transcription	Osteobl	bone
11	chr1:192927400-192929200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:192927600-192928400	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links