Variant report

Variant	rs41944
Chromosome Location	chr7:117961164-117961165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10085904	0.82[CEU][hapmap]
rs1015782	0.85[EUR][1000 genomes]
rs10247768	0.81[CEU][hapmap]
rs11487110	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11766194	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11769403	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11974039	0.81[CEU][hapmap]
rs12537795	0.83[CEU][hapmap]
rs12670769	0.86[EUR][1000 genomes]
rs12706182	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13221114	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13221120	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1548812	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17140984	0.83[CEU][hapmap]
rs17141053	0.83[CEU][hapmap]
rs1859132	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1859133	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2041527	0.86[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs2058418	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2192234	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2215628	0.83[CEU][hapmap]
rs2286865	0.83[CEU][hapmap]
rs2402357	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35708505	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41931	0.81[EUR][1000 genomes]
rs41936	0.80[EUR][1000 genomes]
rs41965	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41981	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41992	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42488	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4260840	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4599745	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730837	0.81[CEU][hapmap]
rs4730853	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730862	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4730866	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5000271	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5002232	0.84[EUR][1000 genomes]
rs61328879	0.89[EUR][1000 genomes]
rs6466648	0.85[EUR][1000 genomes]
rs6466657	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6651117	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6942513	0.91[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs6963274	0.87[CEU][hapmap]
rs6964858	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6964911	0.82[CEU][hapmap]
rs71314617	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs769435	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7786233	0.88[CEU][hapmap]
rs7799229	0.83[CEU][hapmap]
rs881802	0.82[CEU][hapmap]
rs9656259	0.85[EUR][1000 genomes]
rs996726	0.92[EUR][1000 genomes];0.94[ASN][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	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	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41944	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117960600-117961400	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr7:117960800-117961600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr7:117960800-117962000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:117961000-117961200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr7:117961000-117961400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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