Variant report

Variant	rs10880884
Chromosome Location	chr12:46398063-46398064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46382194..46387214-chr12:46392482..46398742,9	MCF-7	breast:
2	chr12:46389987..46392891-chr12:46396271..46398091,2	K562	blood:
3	chr12:46389619..46391753-chr12:46396680..46398448,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCAF11-3	chr12:46397821-46398468	NONHSAT027847

Variant related genes	Relation type
ENSG00000139218	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1012642	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10748438	0.83[YRI][hapmap]
rs10785593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10880875	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10880879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880887	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11183241	0.94[ASN][1000 genomes]
rs11183243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11183268	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11574952	0.85[YRI][hapmap]
rs12314770	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12826749	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1366024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17096380	0.85[YRI][hapmap]
rs1863127	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2059404	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs247917	0.81[ASN][1000 genomes]
rs247918	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs247919	0.83[ASN][1000 genomes]
rs247920	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs247929	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs247930	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs35115	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs35117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs35121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs35122	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs35125	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs6582574	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7134559	0.81[ASN][1000 genomes]
rs724909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7298703	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7306229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7308284	0.81[ASN][1000 genomes]
rs7311198	0.86[AMR][1000 genomes]
rs7315731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7966125	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7967208	0.94[ASN][1000 genomes]
rs7970129	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7971993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976870	0.96[CEU][hapmap]
rs997307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv983463	chr12:46377328-46403983	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46393800-46399400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:46393800-46399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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