Variant report

Variant	rs12510243
Chromosome Location	chr4:80473059-80473060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRDM8-9	chr4:80472781-80474355	NONHSAT097115

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	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022314	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022663	0.85[ASN][1000 genomes]
rs10025630	1.00[ASN][1000 genomes]
rs10027904	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10033410	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1031005	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1074134	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11098741	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098742	0.89[AMR][1000 genomes];0.98[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	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1115518	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs1115519	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11728755	0.84[ASN][1000 genomes]
rs11736348	0.83[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	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs12502224	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506212	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12507160	0.84[ASN][1000 genomes]
rs12507375	0.84[ASN][1000 genomes]
rs12510204	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511646	0.84[ASN][1000 genomes]
rs12511890	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12513177	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639996	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640638	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643491	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13111877	0.86[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	0.82[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	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13146986	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1371993	0.88[ASN][1000 genomes]
rs1371996	0.89[AMR][1000 genomes];0.97[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	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1440862	0.82[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]
rs1440865	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440866	1.00[ASN][1000 genomes]
rs1561638	0.82[ASN][1000 genomes]
rs1561639	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1561640	0.82[ASN][1000 genomes]
rs1595966	0.90[AMR][1000 genomes];0.99[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	0.82[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	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119420	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2119421	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165386	0.84[ASN][1000 genomes]
rs2165387	0.85[ASN][1000 genomes]
rs2165388	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943669	0.86[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	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975054	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975055	0.89[AMR][1000 genomes];0.98[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];0.89[YRI][hapmap]
rs6812760	0.88[ASN][1000 genomes]
rs6850999	0.84[ASN][1000 genomes]
rs6852514	0.84[ASN][1000 genomes]
rs723243	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723245	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7655446	0.82[ASN][1000 genomes]
rs7663844	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7667469	0.84[ASN][1000 genomes]
rs7670107	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7684683	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7690520	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7691021	0.82[ASN][1000 genomes]
rs7697359	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307532	0.84[ASN][1000 genomes]
rs9307545	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs968176	0.84[ASN][1000 genomes]
rs998437	0.84[AMR][1000 genomes];0.97[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
rs12510243	FLJ45337	trans	multi-tissue	Pritchard
rs12510243	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs12510243	PPEF2	cis	parietal	SCAN
rs12510243	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	chr4:80470000-80475200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
4	chr4:80470600-80473400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr4:80471200-80473600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:80471200-80474800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:80471800-80473200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr4:80471800-80473200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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