Variant report

Variant	rs2281012
Chromosome Location	chr6:114671420-114671421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:114662119..114667220-chr6:114669334..114673077,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HS3ST5-3	chr6:114670647-114671812	NONHSAT114609

Variant related genes	Relation type
ENSG00000249853	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10080647	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10155761	0.80[ASN][1000 genomes]
rs10872117	0.94[ASN][1000 genomes]
rs11962755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11964902	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11965041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11968668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1323046	0.94[ASN][1000 genomes]
rs1323047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1323048	0.94[ASN][1000 genomes]
rs1324447	0.81[JPT][hapmap]
rs1337335	0.81[ASN][1000 genomes]
rs1407729	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1408454	0.81[JPT][hapmap]
rs1415428	0.94[ASN][1000 genomes]
rs1415429	0.94[ASN][1000 genomes]
rs1415430	0.94[ASN][1000 genomes]
rs17325929	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17326650	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1819199	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2205737	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2208945	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2224692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349468	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2882172	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945515	0.81[JPT][hapmap]
rs4946001	0.81[JPT][hapmap]
rs56067384	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6917878	0.94[ASN][1000 genomes]
rs6926249	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71028414	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7749363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9320493	0.81[JPT][hapmap]
rs9481441	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488389	0.86[ASN][1000 genomes]
rs9488390	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv428494	chr6:114666307-114774841	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2758074	chr6:114666308-115526957	Enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114666600-114681800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:114667000-114680600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:114667000-114681600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:114668800-114681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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