Variant report

Variant	rs60887734
Chromosome Location	chr3:140307430-140307431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLSTN2-3	chr3:140305717-140307953	l_2484_NR_026783

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1009558	1.00[AMR][1000 genomes]
rs13315403	1.00[AMR][1000 genomes]
rs13316563	1.00[AMR][1000 genomes]
rs13433760	1.00[AMR][1000 genomes]
rs13433933	1.00[AMR][1000 genomes]
rs13434096	1.00[AMR][1000 genomes]
rs1389813	1.00[AMR][1000 genomes]
rs1561766	1.00[AMR][1000 genomes]
rs1567642	1.00[AMR][1000 genomes]
rs1827168	1.00[AMR][1000 genomes]
rs1827169	1.00[AMR][1000 genomes]
rs2119726	0.90[AMR][1000 genomes]
rs2165583	0.83[AMR][1000 genomes]
rs28567961	1.00[AMR][1000 genomes]
rs28569452	1.00[AMR][1000 genomes]
rs28803908	1.00[AMR][1000 genomes]
rs56287987	1.00[AMR][1000 genomes]
rs57787093	1.00[AMR][1000 genomes]
rs58002592	1.00[AMR][1000 genomes]
rs58071968	1.00[AMR][1000 genomes]
rs58294993	1.00[AMR][1000 genomes]
rs59844814	1.00[AMR][1000 genomes]
rs60240007	0.91[AMR][1000 genomes]
rs61598941	1.00[AMR][1000 genomes]
rs61673653	1.00[AMR][1000 genomes]
rs6439937	1.00[AMR][1000 genomes]
rs6763286	1.00[AMR][1000 genomes]
rs6766452	1.00[AMR][1000 genomes]
rs6773423	1.00[AMR][1000 genomes]
rs6790926	1.00[AMR][1000 genomes]
rs6798999	1.00[AMR][1000 genomes]
rs6803694	1.00[AMR][1000 genomes]
rs6806640	1.00[AMR][1000 genomes]
rs72979237	1.00[AMR][1000 genomes]
rs72979242	1.00[AMR][1000 genomes]
rs72979243	1.00[AMR][1000 genomes]
rs72979250	1.00[AMR][1000 genomes]
rs72979253	1.00[AMR][1000 genomes]
rs72981933	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72981959	1.00[AMR][1000 genomes]
rs7430829	1.00[AMR][1000 genomes]
rs7432960	1.00[AMR][1000 genomes]
rs7627138	1.00[AMR][1000 genomes]
rs7639139	1.00[AMR][1000 genomes]
rs7649377	1.00[AMR][1000 genomes]
rs7651804	1.00[AMR][1000 genomes]
rs9289605	1.00[AMR][1000 genomes]
rs9289606	1.00[AMR][1000 genomes]
rs9808968	1.00[AMR][1000 genomes]
rs9813212	1.00[AMR][1000 genomes]
rs9813825	1.00[AMR][1000 genomes]
rs9822864	1.00[AMR][1000 genomes]
rs9823422	1.00[AMR][1000 genomes]
rs9827955	1.00[AMR][1000 genomes]
rs9828653	1.00[AMR][1000 genomes]
rs9828789	1.00[AMR][1000 genomes]
rs9830692	1.00[AMR][1000 genomes]
rs9830840	1.00[AMR][1000 genomes]
rs9834822	0.83[AMR][1000 genomes]
rs9840918	1.00[AMR][1000 genomes]
rs9841078	1.00[AMR][1000 genomes]
rs9843928	1.00[AMR][1000 genomes]
rs9844923	1.00[AMR][1000 genomes]
rs9844924	1.00[AMR][1000 genomes]
rs9857931	1.00[AMR][1000 genomes]
rs9865529	0.91[AMR][1000 genomes]
rs9865940	1.00[AMR][1000 genomes]
rs9868284	1.00[AMR][1000 genomes]
rs9869402	1.00[AMR][1000 genomes]
rs9870785	1.00[AMR][1000 genomes]
rs9872697	1.00[AMR][1000 genomes]
rs9877773	1.00[AMR][1000 genomes]
rs9879403	1.00[AMR][1000 genomes]
rs9879413	1.00[AMR][1000 genomes]
rs9880582	1.00[AMR][1000 genomes]
rs9882754	1.00[AMR][1000 genomes]
rs9883053	1.00[AMR][1000 genomes]
rs9883273	1.00[AMR][1000 genomes]
rs9883666	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv870185	chr3:140265153-140395673	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv877546	chr3:140299603-140468370	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140305800-140307600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:140305800-140307600	Weak transcription	NH-A	brain
3	chr3:140306000-140318200	Weak transcription	HSMM	muscle
4	chr3:140306800-140308000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:140306800-140308400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:140307000-140307600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:140307000-140307800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:140307000-140307800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:140307000-140308000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:140307000-140308400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:140307400-140307800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:140307400-140307800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:140307400-140307800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr3:140307400-140307800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:140307400-140307800	Enhancers	HSMMtube	muscle
16	chr3:140307400-140308000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:140307400-140308000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:140307400-140308000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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