Variant report

Variant	rs11746980
Chromosome Location	chr5:44777878-44777879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:44777877..44780839-chr5:44824446..44826409,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGF10-3	chr5:44777685-44781267	l_2917_chr5:44777367-44844699_brain

Variant related genes	Relation type
ENSG00000272335	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10038562	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10040082	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10040488	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10041518	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10044096	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10045264	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10054773	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10057521	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10059086	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10060878	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10063172	0.80[ASN][1000 genomes]
rs10064434	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10064437	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10065638	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10069220	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10070037	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10072025	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10072259	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10462080	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10462081	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10462082	0.92[ASN][1000 genomes]
rs10462083	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10473376	0.80[ASN][1000 genomes]
rs10473377	0.80[ASN][1000 genomes]
rs1048758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10512865	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1061310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741772	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11746506	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11747159	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750119	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11948387	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11948636	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11949847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11951760	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11957920	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11958451	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11958808	0.87[EUR][1000 genomes]
rs12109710	0.80[ASN][1000 genomes]
rs12188871	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12513749	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12518851	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651949	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12652026	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656984	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13154781	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13155698	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13157608	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13159598	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13160259	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168400	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13174122	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13177711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13183209	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13185174	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13187933	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13189120	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371023	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1371024	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1371025	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1438819	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1438820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438822	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1438827	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16901963	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16901964	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16901965	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16901989	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16901990	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1821934	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866406	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013513	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2083243	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118764	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165008	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2218080	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2218081	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs2330572	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2330619	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2330620	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2877172	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34501299	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3747479	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761648	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761649	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4129642	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4329028	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4395640	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4412123	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4457088	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4457089	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4518409	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4596389	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4642377	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866783	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4866784	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866920	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57300972	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6451772	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451774	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6451775	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451781	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67274820	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6859157	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6867533	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868232	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6868779	0.90[ASN][1000 genomes]
rs6870136	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871820	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6872254	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6875933	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6881563	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6894324	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6896350	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6896417	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714130	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs71610376	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs727304	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs727305	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729599	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7380559	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7449277	0.90[ASN][1000 genomes]
rs7703059	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705343	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7708506	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7710952	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7710978	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7711136	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711697	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712949	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7715731	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7716571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7717459	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7720787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7728431	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730841	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7736952	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737491	0.93[ASN][1000 genomes]
rs920329	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs9292913	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9292914	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9292915	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs930394	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637783	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637796	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637797	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs969679	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790879	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9790896	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791056	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791059	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9791164	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs987394	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880457	chr5:44632008-44800665	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830279	chr5:44688175-44860815	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv597933	chr5:44740989-44810740	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	n/a
5	nsv880712	chr5:44777878-44842260	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11746980	MRPS30	cis	parietal	SCAN
rs11746980	LOC647121	Cis_chr	lymphoblastoid	RTeQTL
rs11746980	RP11-53O19.3	cis	Nerve Tibial	GTEx
rs11746980	MRPS30	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44777400-44780800	Strong transcription	Hela-S3	cervix

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