Variant report

Variant	rs10487392
Chromosome Location	chr7:117872628-117872629
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117858675..117860839-chr7:117870370..117872666,2	K562	blood:
2	chr7:117867427..117869057-chr7:117871203..117872757,2	K562	blood:
3	chr7:117845682..117847702-chr7:117872075..117874755,2	K562	blood:
4	chr7:117858469..117860839-chr7:117870370..117873011,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1015782	0.81[EUR][1000 genomes]
rs10247768	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11487110	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs11542074	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11974039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11983651	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12154684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12670769	0.81[EUR][1000 genomes]
rs1544583	0.88[EUR][1000 genomes]
rs1544584	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17141053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041527	0.81[CEU][hapmap]
rs2058418	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2215628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286863	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28260	0.88[EUR][1000 genomes]
rs33924981	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34010516	0.88[EUR][1000 genomes]
rs34019303	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35218902	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35485182	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41903	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41904	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41912	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41921	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41923	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41924	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41925	0.88[EUR][1000 genomes]
rs41930	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41931	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41936	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41962	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41989	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4260839	0.83[EUR][1000 genomes]
rs45604739	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57308869	0.81[ASN][1000 genomes]
rs61328879	0.84[EUR][1000 genomes]
rs62466471	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466515	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62468297	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62469806	0.85[EUR][1000 genomes]
rs6466648	0.81[EUR][1000 genomes]
rs6942513	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6960940	0.81[EUR][1000 genomes]
rs769435	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7786233	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7801976	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9641593	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9656259	0.81[EUR][1000 genomes]
rs992035	0.84[CEU][hapmap]

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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv889089	chr7:117865940-117921267	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv889090	chr7:117865940-118067460	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10487392	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117872000-117872800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:117872000-117873200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr7:117872400-117873200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:117872400-117873200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr7:117872400-117873800	Enhancers	HMEC	breast
6	chr7:117872600-117873000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:117872600-117873000	Enhancers	NH-A	brain
8	chr7:117872600-117873600	Enhancers	NHEK	skin
9	chr7:117872600-117873800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links