Variant report

Variant	rs55715775
Chromosome Location	chr1:152903063-152903064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRR2D-1	chr1:152902516-152904287	XLOC_001030

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11801965	0.83[AMR][1000 genomes]
rs16834764	1.00[AMR][1000 genomes]
rs16834767	0.92[AFR][1000 genomes]
rs16834768	1.00[AMR][1000 genomes]
rs16834770	0.92[AFR][1000 genomes]
rs56196020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57558489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59432100	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60551318	0.92[AFR][1000 genomes]
rs73006599	0.83[AMR][1000 genomes]
rs74130580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74131105	0.92[AFR][1000 genomes]
rs74131151	0.92[AFR][1000 genomes]
rs74131157	0.92[AFR][1000 genomes]
rs74133823	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74133824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74133825	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74133826	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74133828	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74133829	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7543961	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
8	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152896800-152905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:152903000-152903400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:152903000-152903400	Enhancers	HMEC	breast

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