Variant report

Variant	rs42488
Chromosome Location	chr7:117972361-117972362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10085904	0.84[CEU][hapmap]
rs1015782	0.83[EUR][1000 genomes]
rs10247768	0.88[CEU][hapmap]
rs11487110	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11761947	0.82[EUR][1000 genomes]
rs11766194	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11768889	0.82[EUR][1000 genomes]
rs11769403	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11974039	0.88[CEU][hapmap]
rs11983651	0.85[CEU][hapmap]
rs12537795	0.84[CEU][hapmap]
rs12670769	0.83[EUR][1000 genomes]
rs12706182	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13221114	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13221120	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13224397	0.82[EUR][1000 genomes]
rs1548812	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17140984	0.88[CEU][hapmap]
rs17141053	0.88[CEU][hapmap]
rs17584234	0.81[EUR][1000 genomes]
rs17584359	0.82[EUR][1000 genomes]
rs1859132	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1859133	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194577	0.82[EUR][1000 genomes]
rs194578	0.82[EUR][1000 genomes]
rs194579	0.82[EUR][1000 genomes]
rs2041527	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs2058418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs20598	0.82[EUR][1000 genomes]
rs2192234	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2215628	0.88[CEU][hapmap]
rs2286865	0.88[CEU][hapmap]
rs2402357	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34029977	0.82[EUR][1000 genomes]
rs34847140	0.82[EUR][1000 genomes]
rs35382009	0.82[EUR][1000 genomes]
rs35708505	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41944	0.94[EUR][1000 genomes];0.97[ASN][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]
rs41961	0.82[EUR][1000 genomes]
rs41962	0.84[EUR][1000 genomes]
rs41963	0.82[EUR][1000 genomes]
rs41964	0.82[EUR][1000 genomes]
rs41965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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]
rs41981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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]
rs41989	0.84[EUR][1000 genomes]
rs41990	0.82[EUR][1000 genomes]
rs41991	0.82[EUR][1000 genomes]
rs41992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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]
rs4260839	0.82[EUR][1000 genomes]
rs4260840	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4599745	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727865	0.82[EUR][1000 genomes]
rs4730837	0.88[CEU][hapmap]
rs4730853	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730862	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4730866	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5000271	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5002232	0.82[EUR][1000 genomes]
rs61328879	0.87[EUR][1000 genomes]
rs6466648	0.83[EUR][1000 genomes]
rs6466657	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6651117	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68189275	0.82[EUR][1000 genomes]
rs6942513	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs6963274	0.92[CEU][hapmap]
rs6964858	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6964911	0.87[CEU][hapmap]
rs71314617	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs769435	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs7786233	0.96[CEU][hapmap]
rs7799229	0.84[CEU][hapmap]
rs881801	0.85[CEU][hapmap]
rs881802	0.85[ASW][hapmap];0.84[CEU][hapmap]
rs9656259	0.83[EUR][1000 genomes]
rs996726	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs42488	LSM8	cis	multi-tissue	Pritchard
rs42488	ANKRD7	cis	parietal	SCAN

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	chr7:117970800-117975800	Weak transcription	Dnd41	blood

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