Variant report

Variant	rs2137619
Chromosome Location	chr3:119407403-119407404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1124723	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1124724	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914676	0.89[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs11923223	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes]
rs12490779	0.92[CEU][hapmap]
rs12492456	0.83[CHB][hapmap]
rs12493022	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13061374	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13061497	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13062540	0.80[JPT][hapmap]
rs13065893	0.80[JPT][hapmap]
rs1403631	0.89[CHB][hapmap]
rs16830291	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes]
rs17203235	0.92[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs1851611	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1872432	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap]
rs1880040	0.80[JPT][hapmap]
rs1905788	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1905790	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1985121	0.89[CHB][hapmap]
rs2102627	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280578	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs2629395	0.80[JPT][hapmap]
rs2629409	0.80[JPT][hapmap]
rs2670292	0.89[CHB][hapmap]
rs2688629	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap]
rs2688631	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap]
rs2698281	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749416	0.80[JPT][hapmap]
rs3772134	0.80[JPT][hapmap]
rs3844090	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3924065	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234662	0.83[CHB][hapmap]
rs4327424	0.80[JPT][hapmap]
rs4485753	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4585237	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4629367	0.83[AMR][1000 genomes]
rs4688021	0.89[CHB][hapmap]
rs4688023	0.80[JPT][hapmap]
rs4688024	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs523476	0.80[JPT][hapmap]
rs524043	0.89[CHB][hapmap]
rs525916	0.88[CHB][hapmap]
rs540420	0.89[CHB][hapmap]
rs552244	0.80[JPT][hapmap]
rs56042515	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572119	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs575833	0.87[CHB][hapmap]
rs6438542	0.80[JPT][hapmap]
rs6766563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6783324	0.89[CHB][hapmap]
rs6792417	0.90[AMR][1000 genomes]
rs6794579	0.82[JPT][hapmap]
rs6803814	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs68150601	0.84[AMR][1000 genomes]
rs71325397	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7626940	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8007	0.80[JPT][hapmap]
rs8422	0.83[CHB][hapmap]
rs940182	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs940183	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers 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	12 gene(s)	inside rSNPs	diseases
5	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3358659	chr3:119402929-119414857	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv591391	chr3:119403145-119442572	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2137619	ILDR1	cis	cerebellum	SCAN
rs2137619	COX17	cis	lymphoblastoid	seeQTL
rs2137619	COX17	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119406000-119421400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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