Variant report

Variant	rs2042555
Chromosome Location	chr2:148555489-148555490
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	chr2:148548328..148550845-chr2:148553966..148555701,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10180655	0.87[CEU][hapmap]
rs12622150	0.89[CEU][hapmap];0.89[LWK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs13016400	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13016893	0.84[CEU][hapmap]
rs13430086	0.84[CEU][hapmap]
rs1895694	0.89[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs2113792	0.85[CEU][hapmap]
rs2113794	0.80[EUR][1000 genomes]
rs2194695	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2603600	0.83[TSI][hapmap]
rs3768684	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs3768686	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs3768688	0.89[CEU][hapmap]
rs55816333	0.87[EUR][1000 genomes]
rs56073268	0.83[EUR][1000 genomes]
rs6709182	0.92[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6713811	0.89[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs6731371	0.82[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs755365	0.95[ASN][1000 genomes]
rs7566230	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7582403	0.89[CEU][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9287411	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs998884	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2042555	ACVR2A	cis	parietal	SCAN
rs2042555	ORC4L	Cis_1M	lymphoblastoid	RTeQTL
rs2042555	ACVR2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148550200-148556200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:148551600-148555600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:148553800-148555600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:148553800-148555600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:148554000-148555600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr2:148554000-148555600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:148554400-148556800	Enhancers	HSMM	muscle
8	chr2:148554600-148556600	Enhancers	HSMMtube	muscle
9	chr2:148555000-148555800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:148555400-148556600	Enhancers	Muscle Satellite Cultured Cells	--

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