Variant report

Variant	rs1878993
Chromosome Location	chr3:135527891-135527892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSL2-5	chr3:135527258-135528059	l_2480_chr3:135527257-135528916_breast

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11916990	1.00[ASN][1000 genomes]
rs1401543	1.00[ASN][1000 genomes]
rs16843365	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17195888	1.00[ASN][1000 genomes]
rs17196014	1.00[ASN][1000 genomes]
rs17196097	1.00[ASN][1000 genomes]
rs17249203	1.00[ASN][1000 genomes]
rs2176666	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895793	1.00[ASN][1000 genomes]
rs34629706	1.00[ASN][1000 genomes]
rs56380708	0.88[EUR][1000 genomes]
rs56382648	1.00[ASN][1000 genomes]
rs56818259	1.00[ASN][1000 genomes]
rs57767257	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57895104	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59165430	0.85[EUR][1000 genomes]
rs60349283	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60545022	1.00[ASN][1000 genomes]
rs61789012	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789017	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789024	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61789025	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61789026	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790390	1.00[ASN][1000 genomes]
rs61790396	1.00[ASN][1000 genomes]
rs61790400	1.00[ASN][1000 genomes]
rs61790401	1.00[ASN][1000 genomes]
rs61790403	1.00[ASN][1000 genomes]
rs61790404	1.00[ASN][1000 genomes]
rs61790457	1.00[ASN][1000 genomes]
rs61790458	1.00[ASN][1000 genomes]
rs61790459	1.00[ASN][1000 genomes]
rs6414336	1.00[ASN][1000 genomes]
rs6762218	1.00[ASN][1000 genomes]
rs6765327	1.00[ASN][1000 genomes]
rs6769033	1.00[ASN][1000 genomes]
rs6769893	1.00[ASN][1000 genomes]
rs6786217	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802942	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72977660	1.00[ASN][1000 genomes]
rs73863014	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73863035	1.00[ASN][1000 genomes]
rs7618257	1.00[ASN][1000 genomes]
rs7635010	1.00[ASN][1000 genomes]
rs908827	1.00[ASN][1000 genomes]
rs980210	1.00[ASN][1000 genomes]
rs9865234	1.00[CHB][hapmap]

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	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135525600-135528000	Weak transcription	Fetal Brain Female	brain
2	chr3:135526400-135528200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:135527200-135529400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:135527400-135528600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:135527800-135528800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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