Variant report

Variant	rs41926
Chromosome Location	chr7:117921576-117921577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:117916864..117919001-chr7:117920265..117922583,2	MCF-7	breast:

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10085904	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs10226152	0.90[EUR][1000 genomes]
rs10227326	0.90[EUR][1000 genomes]
rs10229589	0.90[EUR][1000 genomes]
rs10252627	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10267938	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10487390	0.90[EUR][1000 genomes]
rs1054032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1061731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10953864	0.84[EUR][1000 genomes]
rs1117254	0.86[EUR][1000 genomes]
rs11486992	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11543742	0.89[EUR][1000 genomes]
rs11761947	0.82[EUR][1000 genomes]
rs11768889	0.82[EUR][1000 genomes]
rs11770353	0.87[EUR][1000 genomes]
rs11979012	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs12112697	0.88[CEU][hapmap]
rs12537795	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs12667103	0.94[EUR][1000 genomes]
rs13224397	0.82[EUR][1000 genomes]
rs13224733	0.92[EUR][1000 genomes]
rs17584234	0.81[EUR][1000 genomes]
rs17584359	0.82[EUR][1000 genomes]
rs194577	0.82[EUR][1000 genomes]
rs194578	0.82[EUR][1000 genomes]
rs194579	0.82[EUR][1000 genomes]
rs2041527	0.84[CEU][hapmap]
rs2058416	0.87[EUR][1000 genomes]
rs2058417	0.92[EUR][1000 genomes]
rs20598	0.82[EUR][1000 genomes]
rs2191920	0.87[EUR][1000 genomes]
rs2402322	0.90[EUR][1000 genomes]
rs2896242	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs34029977	0.82[EUR][1000 genomes]
rs34847140	0.82[EUR][1000 genomes]
rs35382009	0.82[EUR][1000 genomes]
rs3802012	0.88[EUR][1000 genomes]
rs4141028	0.88[EUR][1000 genomes]
rs41900	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41901	0.96[EUR][1000 genomes]
rs41902	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41905	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41906	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41908	0.80[EUR][1000 genomes]
rs41909	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41910	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41911	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41915	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41916	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41933	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41934	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41935	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41938	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41939	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41945	0.85[EUR][1000 genomes]
rs41946	0.82[EUR][1000 genomes]
rs41947	0.82[EUR][1000 genomes]
rs41948	0.82[EUR][1000 genomes]
rs41949	0.82[EUR][1000 genomes]
rs41950	0.82[EUR][1000 genomes]
rs41951	0.82[EUR][1000 genomes]
rs41952	0.82[EUR][1000 genomes]
rs41953	0.82[EUR][1000 genomes]
rs41954	0.82[EUR][1000 genomes]
rs41955	0.82[EUR][1000 genomes]
rs41956	0.82[EUR][1000 genomes]
rs41957	0.82[EUR][1000 genomes]
rs41958	0.82[EUR][1000 genomes]
rs41959	0.81[EUR][1000 genomes]
rs41960	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41961	0.82[EUR][1000 genomes]
rs41963	0.82[EUR][1000 genomes]
rs41964	0.82[EUR][1000 genomes]
rs41966	0.81[EUR][1000 genomes]
rs41967	0.82[EUR][1000 genomes]
rs41968	0.82[EUR][1000 genomes]
rs41969	0.82[EUR][1000 genomes]
rs41970	0.82[EUR][1000 genomes]
rs41977	0.82[EUR][1000 genomes]
rs41978	0.80[EUR][1000 genomes]
rs41979	0.82[EUR][1000 genomes]
rs41980	0.82[EUR][1000 genomes]
rs41982	0.82[EUR][1000 genomes]
rs41983	0.82[EUR][1000 genomes]
rs41984	0.82[EUR][1000 genomes]
rs41985	0.82[EUR][1000 genomes]
rs41986	0.82[EUR][1000 genomes]
rs41987	0.82[EUR][1000 genomes]
rs41988	0.82[EUR][1000 genomes]
rs41990	0.82[EUR][1000 genomes]
rs41991	0.82[EUR][1000 genomes]
rs41993	0.82[EUR][1000 genomes]
rs41994	0.82[EUR][1000 genomes]
rs41995	0.82[EUR][1000 genomes]
rs41996	0.82[EUR][1000 genomes]
rs41997	0.82[EUR][1000 genomes]
rs42234	0.82[EUR][1000 genomes]
rs42376	0.82[EUR][1000 genomes]
rs4727865	0.82[EUR][1000 genomes]
rs5002233	0.90[EUR][1000 genomes]
rs68189275	0.82[EUR][1000 genomes]
rs6942513	0.84[CEU][hapmap]
rs6944524	0.90[EUR][1000 genomes]
rs6946855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6948096	0.90[EUR][1000 genomes]
rs6956486	0.84[EUR][1000 genomes]
rs6964911	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs6965144	0.90[EUR][1000 genomes]
rs7779933	0.83[EUR][1000 genomes]
rs7796145	0.90[EUR][1000 genomes]
rs7796148	0.90[EUR][1000 genomes]
rs7797855	0.90[EUR][1000 genomes]
rs7799229	0.92[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs7806490	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs881802	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs917761	0.85[EUR][1000 genomes]
rs9655829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9656260	0.84[EUR][1000 genomes]
rs979652	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs989899	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	nsv889091	chr7:117899190-117963926	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1029103	chr7:117917362-118035987	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2764014	chr7:117917374-118035999	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv608261	chr7:117917719-117965390	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv518701	chr7:117921267-117928764	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3350080	chr7:117921328-117921626	Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41926	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117919600-117922600	Enhancers	Dnd41	blood
2	chr7:117920200-117921600	Enhancers	Fetal Intestine Small	intestine
3	chr7:117921000-117921800	Enhancers	Duodenum Mucosa	Duodenum
4	chr7:117921000-117922000	Enhancers	HUVEC	blood vessel
5	chr7:117921200-117921600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr7:117921400-117921800	Enhancers	Fetal Intestine Large	intestine

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