Variant report

Variant	rs41980
Chromosome Location	chr7:117985261-117985262
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10085904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10252627	0.84[EUR][1000 genomes]
rs1054032	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs1061731	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs10953864	0.81[EUR][1000 genomes]
rs11486992	0.92[CEU][hapmap]
rs11761947	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766194	0.82[EUR][1000 genomes]
rs11768889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11769403	0.82[EUR][1000 genomes]
rs11979012	0.91[CEU][hapmap];0.80[CHB][hapmap]
rs12537795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs12706182	0.82[EUR][1000 genomes]
rs13221114	0.82[EUR][1000 genomes]
rs13221120	0.82[EUR][1000 genomes]
rs13224397	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13236353	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17584234	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17584359	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859132	0.81[EUR][1000 genomes]
rs1859133	0.81[EUR][1000 genomes]
rs194577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs194578	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs194579	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058418	0.84[CEU][hapmap]
rs20598	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192233	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2402353	0.81[EUR][1000 genomes]
rs2402359	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2896242	0.88[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap]
rs34029977	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34847140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35382009	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35708505	0.82[EUR][1000 genomes]
rs41910	0.81[EUR][1000 genomes]
rs41911	0.81[EUR][1000 genomes]
rs41915	0.82[EUR][1000 genomes]
rs41916	0.82[EUR][1000 genomes]
rs41926	0.82[EUR][1000 genomes]
rs41933	0.85[EUR][1000 genomes]
rs41934	0.87[EUR][1000 genomes]
rs41935	0.87[EUR][1000 genomes]
rs41938	0.87[EUR][1000 genomes]
rs41939	0.87[EUR][1000 genomes]
rs41945	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41946	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41947	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41948	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41949	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41950	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41951	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41952	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41953	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41954	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41955	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41957	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41959	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41960	0.93[EUR][1000 genomes]
rs41961	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41963	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41964	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41965	0.82[EUR][1000 genomes]
rs41966	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41968	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41969	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41977	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41981	0.82[EUR][1000 genomes]
rs41982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41985	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41986	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41987	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41988	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41992	0.82[EUR][1000 genomes]
rs41993	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41995	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41996	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41997	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42234	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42488	0.82[EUR][1000 genomes]
rs4260840	0.80[EUR][1000 genomes]
rs4599745	0.82[EUR][1000 genomes]
rs4727865	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730853	0.82[EUR][1000 genomes]
rs5000271	0.80[EUR][1000 genomes]
rs68189275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942513	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6946855	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6956486	0.81[EUR][1000 genomes]
rs6964911	0.84[CEU][hapmap]
rs7779933	0.81[EUR][1000 genomes]
rs7799229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7805314	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs881802	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs917761	0.82[EUR][1000 genomes]
rs9655829	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs9656260	0.81[EUR][1000 genomes]
rs979652	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs992035	0.87[CEU][hapmap]
rs996726	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	nsv608262	chr7:117926753-118036133	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv429805	chr7:117940049-118026049	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1804964	chr7:117960973-118188573	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1803022	chr7:117970170-117998574	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv608263	chr7:117973445-118058927	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv889092	chr7:117977091-118067460	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv889093	chr7:117977091-118709754	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv889094	chr7:117981820-118186543	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv966731	chr7:117985186-117987623	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41980	LSM8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117964400-117986800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:117984600-117986200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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