Variant report

Variant	rs1440865
Chromosome Location	chr4:80469901-80469902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10004226	0.84[ASN][1000 genomes]
rs10022309	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022314	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022663	0.85[ASN][1000 genomes]
rs10025630	1.00[ASN][1000 genomes]
rs10027904	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10033410	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1031005	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1074134	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11098741	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098742	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098762	0.84[ASN][1000 genomes]
rs11098764	0.84[ASN][1000 genomes]
rs11098766	0.84[ASN][1000 genomes]
rs11098770	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1115518	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1115519	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11728755	0.84[ASN][1000 genomes]
rs11736348	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11736369	0.85[ASN][1000 genomes]
rs11936123	0.82[ASN][1000 genomes]
rs11941782	0.88[ASN][1000 genomes]
rs12500146	0.84[ASN][1000 genomes]
rs12501981	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs12502224	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506212	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12507160	0.84[ASN][1000 genomes]
rs12507375	0.84[ASN][1000 genomes]
rs12510204	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510243	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511646	0.84[ASN][1000 genomes]
rs12511890	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12513177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639996	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640638	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643491	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13111877	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13112067	0.88[ASN][1000 genomes]
rs13112577	0.88[ASN][1000 genomes]
rs13118924	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13127970	0.80[ASN][1000 genomes]
rs13128134	1.00[ASN][1000 genomes]
rs13144408	0.95[ASN][1000 genomes]
rs13146986	0.85[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1371993	0.88[ASN][1000 genomes]
rs1371996	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1440852	0.84[ASN][1000 genomes]
rs1440853	0.84[ASN][1000 genomes]
rs1440854	0.84[ASN][1000 genomes]
rs1440860	0.84[ASN][1000 genomes]
rs1440861	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1440862	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1440863	0.82[ASN][1000 genomes]
rs1440864	0.84[ASN][1000 genomes]
rs1440866	1.00[ASN][1000 genomes]
rs1561638	0.82[ASN][1000 genomes]
rs1561639	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1561640	0.82[ASN][1000 genomes]
rs1595966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837645	0.88[ASN][1000 genomes]
rs1837646	0.88[ASN][1000 genomes]
rs1837647	0.96[ASN][1000 genomes]
rs1899232	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1975399	0.84[ASN][1000 genomes]
rs1992367	0.98[ASN][1000 genomes]
rs2119419	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119420	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119421	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165386	0.84[ASN][1000 genomes]
rs2165387	0.85[ASN][1000 genomes]
rs2165388	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943669	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4389603	0.85[ASN][1000 genomes]
rs4443312	0.88[ASN][1000 genomes]
rs4583785	0.84[ASN][1000 genomes]
rs4975052	0.82[ASN][1000 genomes]
rs4975053	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975054	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975055	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975056	0.87[ASN][1000 genomes]
rs4975057	0.85[ASN][1000 genomes]
rs4975089	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6812760	0.88[ASN][1000 genomes]
rs6850999	0.84[ASN][1000 genomes]
rs6852514	0.84[ASN][1000 genomes]
rs723243	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723245	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7655446	0.82[ASN][1000 genomes]
rs7663844	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7667469	0.84[ASN][1000 genomes]
rs7670107	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7684683	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7690520	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7691021	0.82[ASN][1000 genomes]
rs7697359	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307532	0.84[ASN][1000 genomes]
rs9307545	0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs968176	0.84[ASN][1000 genomes]
rs998437	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9993773	0.87[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	nsv999174	chr4:80212935-80512356	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1440865	PPEF2	cis	parietal	SCAN
rs1440865	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs1440865	LINC00989	cis	Adipose Subcutaneous	GTEx
rs1440865	LINC00989	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80465000-80478200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:80467600-80485600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:80468400-80470000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:80468400-80471800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:80469200-80470600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:80469400-80470200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:80469400-80471800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:80469600-80470000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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