Variant report

Variant	rs41962
Chromosome Location	chr7:117976279-117976280
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10247768	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs10487392	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11487110	0.83[CEU][hapmap]
rs11542074	0.82[EUR][1000 genomes]
rs11766194	0.82[EUR][1000 genomes]
rs11769403	0.82[EUR][1000 genomes]
rs11974039	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11983651	0.87[CEU][hapmap];0.88[GIH][hapmap]
rs12154684	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs12706182	0.83[EUR][1000 genomes]
rs13221114	0.82[EUR][1000 genomes]
rs13221120	0.82[EUR][1000 genomes]
rs1544584	0.82[EUR][1000 genomes]
rs17140984	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[EUR][1000 genomes]
rs17141053	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs1859132	0.81[EUR][1000 genomes]
rs1859133	0.81[EUR][1000 genomes]
rs2215628	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs2286863	0.82[EUR][1000 genomes]
rs2286865	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs2402353	0.81[EUR][1000 genomes]
rs28260	0.86[EUR][1000 genomes]
rs33924981	0.82[EUR][1000 genomes]
rs34019303	0.82[EUR][1000 genomes]
rs35218902	0.84[EUR][1000 genomes]
rs35485182	0.81[EUR][1000 genomes]
rs35708505	0.84[EUR][1000 genomes]
rs41903	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41904	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41912	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41921	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41923	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41924	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41925	0.86[EUR][1000 genomes]
rs41930	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41931	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41936	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41965	0.84[EUR][1000 genomes]
rs41981	0.84[EUR][1000 genomes]
rs41989	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41992	0.84[EUR][1000 genomes]
rs42488	0.84[EUR][1000 genomes]
rs4260839	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4260840	0.81[EUR][1000 genomes]
rs45604739	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4599745	0.84[EUR][1000 genomes]
rs4730837	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs4730853	0.84[EUR][1000 genomes]
rs4730868	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5000271	0.81[EUR][1000 genomes]
rs62466471	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62466515	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62468297	0.80[EUR][1000 genomes]
rs6960940	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7786233	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7801976	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7811687	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs881801	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs9641593	0.82[EUR][1000 genomes]
rs992035	0.87[CEU][hapmap]
rs996726	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41962	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 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	chr7:117975800-117977400	Enhancers	Dnd41	blood
3	chr7:117976200-117976800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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