Variant report

Variant	rs9656259
Chromosome Location	chr7:117839180-117839181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117834706..117839817-chr7:117854613..117858941,5	K562	blood:
2	chr7:117838537..117840659-chr7:117840686..117843099,2	MCF-7	breast:
3	chr7:117836027..117837598-chr7:117839137..117840763,2	MCF-7	breast:
4	chr7:117792505..117794134-chr7:117837460..117839603,2	K562	blood:

Variant related genes	Relation type
ENSG00000106013	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10085904	0.83[EUR][1000 genomes]
rs1015782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247768	0.86[EUR][1000 genomes]
rs10487392	0.81[EUR][1000 genomes]
rs10953864	0.82[EUR][1000 genomes]
rs11487110	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11542074	0.86[EUR][1000 genomes]
rs11974039	0.80[EUR][1000 genomes]
rs12154684	0.83[EUR][1000 genomes]
rs12537795	0.82[EUR][1000 genomes]
rs12670769	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12706182	0.81[EUR][1000 genomes]
rs1544584	0.85[EUR][1000 genomes]
rs17140984	0.85[EUR][1000 genomes]
rs17141053	0.83[EUR][1000 genomes]
rs2041527	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2058418	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215628	0.86[EUR][1000 genomes]
rs2286863	0.86[EUR][1000 genomes]
rs33924981	0.86[EUR][1000 genomes]
rs34019303	0.86[EUR][1000 genomes]
rs35218902	0.84[EUR][1000 genomes]
rs35485182	0.83[EUR][1000 genomes]
rs35708505	0.83[EUR][1000 genomes]
rs41944	0.85[EUR][1000 genomes]
rs41965	0.83[EUR][1000 genomes]
rs41981	0.83[EUR][1000 genomes]
rs41992	0.83[EUR][1000 genomes]
rs42488	0.83[EUR][1000 genomes]
rs45604739	0.86[EUR][1000 genomes]
rs4599745	0.83[EUR][1000 genomes]
rs4730837	0.85[EUR][1000 genomes]
rs4730853	0.83[EUR][1000 genomes]
rs5002232	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61328879	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62466471	0.84[EUR][1000 genomes]
rs62466515	0.86[EUR][1000 genomes]
rs62468297	0.83[EUR][1000 genomes]
rs6466648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942513	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6956486	0.82[EUR][1000 genomes]
rs769435	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779933	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7786233	0.83[EUR][1000 genomes]
rs7799229	0.81[EUR][1000 genomes]
rs9641593	0.85[EUR][1000 genomes]
rs9656260	0.82[EUR][1000 genomes]
rs996726	0.82[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9656259	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
2	chr7:117825800-117842600	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:117829800-117840800	Weak transcription	Primary T cells from cord blood	blood
4	chr7:117830400-117842400	Weak transcription	Fetal Lung	lung
5	chr7:117831200-117842400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:117831400-117839800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:117832800-117842200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:117833000-117854000	Weak transcription	HSMM	muscle
9	chr7:117833400-117842200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:117833600-117854000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:117834000-117839400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:117834000-117842000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:117834400-117843400	Weak transcription	Fetal Thymus	thymus
14	chr7:117838800-117839400	Strong transcription	Primary B cells from cord blood	blood

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