Variant report

Variant	rs12511646
Chromosome Location	chr4:80499854-80499855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10004226	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022309	0.84[ASN][1000 genomes]
rs10022314	0.84[ASN][1000 genomes]
rs10022663	0.99[ASN][1000 genomes]
rs10025630	0.84[ASN][1000 genomes]
rs10033410	0.84[ASN][1000 genomes]
rs1031004	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1031005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11098741	0.84[ASN][1000 genomes]
rs11098742	0.84[ASN][1000 genomes]
rs11098762	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098764	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098766	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098770	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1115518	0.85[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1115519	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs11728755	0.92[ASN][1000 genomes]
rs11736369	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941782	0.96[ASN][1000 genomes]
rs12500146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501981	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12502224	0.84[ASN][1000 genomes]
rs12507160	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510204	0.84[ASN][1000 genomes]
rs12510243	0.84[ASN][1000 genomes]
rs12513177	0.84[ASN][1000 genomes]
rs12639996	0.84[ASN][1000 genomes]
rs12640638	0.84[ASN][1000 genomes]
rs12643491	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12643976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13104009	0.94[ASN][1000 genomes]
rs13112067	0.96[ASN][1000 genomes]
rs13112577	0.96[ASN][1000 genomes]
rs13124357	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127970	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13128134	0.84[ASN][1000 genomes]
rs13129838	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13142610	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13144408	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13146986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1348086	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371989	0.94[ASN][1000 genomes]
rs1371993	0.96[ASN][1000 genomes]
rs1371996	0.83[ASN][1000 genomes]
rs1440852	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440853	1.00[ASN][1000 genomes]
rs1440854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440865	0.84[ASN][1000 genomes]
rs1440866	0.84[ASN][1000 genomes]
rs1595966	0.84[ASN][1000 genomes]
rs17003985	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837645	0.96[ASN][1000 genomes]
rs1837646	0.96[ASN][1000 genomes]
rs1837647	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1975399	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992367	0.82[ASN][1000 genomes]
rs2119421	0.82[ASN][1000 genomes]
rs2165386	1.00[ASN][1000 genomes]
rs2165387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165388	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2196978	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2867672	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2903640	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35487709	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35631270	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3943669	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4389603	0.99[ASN][1000 genomes]
rs4443312	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4583785	0.81[AMR][1000 genomes]
rs4975053	0.84[ASN][1000 genomes]
rs4975054	0.84[ASN][1000 genomes]
rs4975055	0.84[ASN][1000 genomes]
rs4975056	0.95[ASN][1000 genomes]
rs4975057	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4975089	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4975097	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812760	0.96[ASN][1000 genomes]
rs6850999	1.00[ASN][1000 genomes]
rs6852514	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71629061	0.85[ASN][1000 genomes]
rs7667469	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697359	0.84[ASN][1000 genomes]
rs9307545	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9307551	0.94[ASN][1000 genomes]
rs968176	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12511646	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs12511646	LINC00989	cis	Whole Blood	GTEx
rs12511646	PRKG2	cis	parietal	SCAN
rs12511646	LINC00989	cis	Adipose Subcutaneous	GTEx
rs12511646	LINC00989	cis	Muscle Skeletal	GTEx
rs12511646	LINC00989	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80497600-80506200	Weak transcription	Placenta	Placenta
2	chr4:80499000-80500200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr4:80499000-80500200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:80499000-80500400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr4:80499000-80500400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:80499400-80500200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr4:80499800-80500400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr4:80499800-80500600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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