Variant report

Variant	rs2119090
Chromosome Location	chr2:189025977-189025978
allele	A/G
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:114)

rs_ID	r²[population]
rs10175838	1.00[CHB][hapmap]
rs10180000	1.00[CHB][hapmap]
rs10189197	1.00[CHB][hapmap]
rs10209424	1.00[CHB][hapmap]
rs10460382	0.81[EUR][1000 genomes]
rs10469734	1.00[CHB][hapmap]
rs10931328	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10931329	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931330	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10931331	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10931332	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682297	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11684826	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11687382	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465138	0.87[AMR][1000 genomes]
rs12468413	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12478374	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12615631	0.81[EUR][1000 genomes]
rs12693490	1.00[CHB][hapmap]
rs12693491	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs12693492	1.00[CHB][hapmap]
rs12693493	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs12693497	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs12995107	0.86[ASN][1000 genomes]
rs12995166	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12996638	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13003972	1.00[CHB][hapmap]
rs13011049	0.86[ASN][1000 genomes]
rs13017543	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13021054	0.83[EUR][1000 genomes]
rs13021984	0.88[EUR][1000 genomes]
rs13022215	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024023	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs13027148	0.91[ASN][1000 genomes]
rs13029662	0.86[ASN][1000 genomes]
rs13032231	1.00[CHB][hapmap]
rs13035864	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1304011	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382200	1.00[CHB][hapmap]
rs13390401	1.00[CHB][hapmap]
rs13394232	1.00[CHB][hapmap]
rs13403228	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs13429075	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs1371517	0.87[AMR][1000 genomes]
rs1371518	0.87[AMR][1000 genomes]
rs1371526	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1371527	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1371528	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1371529	0.90[EUR][1000 genomes]
rs1371530	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1439888	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1439889	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1439894	0.87[AMR][1000 genomes]
rs1439903	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1439904	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1439905	0.87[AMR][1000 genomes]
rs1439909	0.90[EUR][1000 genomes]
rs16829839	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1821998	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004888	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs2043946	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2119091	0.87[AMR][1000 genomes]
rs2119093	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2218148	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2350565	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2350566	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2350569	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882449	0.91[ASN][1000 genomes]
rs34142137	0.80[ASN][1000 genomes]
rs34353529	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs34395949	0.86[ASN][1000 genomes]
rs35311707	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35355034	0.86[ASN][1000 genomes]
rs35699394	0.86[ASN][1000 genomes]
rs35823311	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128404	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs4427987	0.89[EUR][1000 genomes]
rs4450571	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4535011	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs4666754	0.92[EUR][1000 genomes]
rs4667212	0.81[EUR][1000 genomes]
rs4667219	1.00[CHB][hapmap]
rs4667220	1.00[CHB][hapmap]
rs55755436	0.83[EUR][1000 genomes]
rs58176375	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61071123	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62179560	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62180847	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6434262	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6434277	1.00[CHB][hapmap]
rs6707652	0.88[EUR][1000 genomes]
rs6707875	0.87[AMR][1000 genomes]
rs6715740	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6718697	1.00[CHB][hapmap]
rs6720983	1.00[CHB][hapmap]
rs6723998	0.88[EUR][1000 genomes]
rs6726233	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6738105	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6742606	0.81[AMR][1000 genomes]
rs6744309	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6745829	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749283	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749627	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6756131	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7571197	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs7571494	1.00[CHB][hapmap]
rs920408	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9288151	1.00[CHB][hapmap]
rs9288152	1.00[CHB][hapmap]
rs971268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs9808523	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs9808557	1.00[CHB][hapmap]
rs997044	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs997045	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875603	chr2:188923773-189025977	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv875604	chr2:188957640-189043137	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv875605	chr2:189017499-189080087	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv521460	chr2:189025977-189046900	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2119090	MEGF9	trans	cerebellum	SCAN
rs2119090	INPP1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189004600-189026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:189025200-189026600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr2:189025800-189030800	Active TSS	ES-I3 Cell Line	embryonic stem cell

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