Variant report

Variant	rs6481773
Chromosome Location	chr10:19463367-19463368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10508576	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10763873	0.86[ASN][1000 genomes]
rs10763889	0.86[ASN][1000 genomes]
rs10763890	0.84[ASN][1000 genomes]
rs10763892	0.86[ASN][1000 genomes]
rs10826990	0.88[ASN][1000 genomes]
rs10826991	0.83[ASN][1000 genomes]
rs10826993	0.88[ASN][1000 genomes]
rs10826996	0.86[ASN][1000 genomes]
rs10826998	0.86[ASN][1000 genomes]
rs10826999	0.86[ASN][1000 genomes]
rs10827111	0.86[ASN][1000 genomes]
rs10827122	0.86[ASN][1000 genomes]
rs11008639	0.86[ASN][1000 genomes]
rs11008846	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11008904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs12240337	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12243775	0.86[ASN][1000 genomes]
rs12250334	0.95[ASN][1000 genomes]
rs12265785	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12354759	0.86[ASN][1000 genomes]
rs12359699	0.90[ASN][1000 genomes]
rs12570472	0.83[EUR][1000 genomes]
rs12570966	0.83[EUR][1000 genomes]
rs12762251	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12767380	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12769479	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12769501	0.86[ASN][1000 genomes]
rs12773103	0.86[ASN][1000 genomes]
rs12775323	0.88[ASN][1000 genomes]
rs12779141	0.88[ASN][1000 genomes]
rs12779623	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12781273	0.93[ASN][1000 genomes]
rs12783745	0.83[EUR][1000 genomes]
rs1591329	0.95[ASN][1000 genomes]
rs16918302	0.86[ASN][1000 genomes]
rs17721336	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17722015	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1889514	0.95[ASN][1000 genomes]
rs2358338	0.88[ASN][1000 genomes]
rs2358339	0.86[ASN][1000 genomes]
rs2358340	0.86[ASN][1000 genomes]
rs2358341	0.85[EUR][1000 genomes]
rs2358344	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2583646	0.91[ASN][1000 genomes]
rs2884431	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34129683	0.85[EUR][1000 genomes]
rs34162471	0.88[ASN][1000 genomes]
rs34280396	0.86[ASN][1000 genomes]
rs34398776	0.83[EUR][1000 genomes]
rs34572308	0.96[ASN][1000 genomes]
rs34724539	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34880376	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35065389	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35139662	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35432267	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4259740	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4320861	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4351724	0.91[ASN][1000 genomes]
rs4364958	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4445549	0.85[ASN][1000 genomes]
rs4466729	0.88[ASN][1000 genomes]
rs4472834	0.88[ASN][1000 genomes]
rs4477351	0.86[ASN][1000 genomes]
rs4491125	0.86[ASN][1000 genomes]
rs4607972	0.83[ASN][1000 genomes]
rs4748558	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4748561	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4748563	0.95[ASN][1000 genomes]
rs57020628	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58095759	0.86[ASN][1000 genomes]
rs60970424	0.96[ASN][1000 genomes]
rs61481867	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6481761	0.86[ASN][1000 genomes]
rs6481762	0.86[ASN][1000 genomes]
rs6481763	0.86[ASN][1000 genomes]
rs6481764	0.86[ASN][1000 genomes]
rs67664564	0.83[ASN][1000 genomes]
rs7070471	0.93[ASN][1000 genomes]
rs7080208	0.88[ASN][1000 genomes]
rs7081923	0.86[ASN][1000 genomes]
rs7084827	0.88[ASN][1000 genomes]
rs7087763	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092667	0.86[ASN][1000 genomes]
rs7092998	0.86[ASN][1000 genomes]
rs7093764	0.88[ASN][1000 genomes]
rs7097491	0.96[ASN][1000 genomes]
rs7097878	0.86[ASN][1000 genomes]
rs7098738	0.86[ASN][1000 genomes]
rs71472841	0.83[ASN][1000 genomes]
rs73593854	0.86[ASN][1000 genomes]
rs73593856	0.86[ASN][1000 genomes]
rs7477457	0.86[ASN][1000 genomes]
rs7894157	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896381	0.86[ASN][1000 genomes]
rs7898234	0.86[ASN][1000 genomes]
rs7906085	0.86[ASN][1000 genomes]
rs7913024	0.86[ASN][1000 genomes]
rs7916470	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427857	chr10:19253828-19599493	Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv894917	chr10:19259024-19463367	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv550126	chr10:19270068-19572729	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv894918	chr10:19390046-19466344	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv466764	chr10:19400845-19979434	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv550128	chr10:19400845-19979434	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv2750885	chr10:19407891-19836364	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1043780	chr10:19415575-19827284	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1035870	chr10:19415575-19832047	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv550129	chr10:19417181-19834795	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1035591	chr10:19417883-19823164	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv540506	chr10:19417883-19823164	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv2750886	chr10:19432774-19832094	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv831802	chr10:19449261-19585888	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv430133	chr10:19452640-19490727	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv428552	chr10:19457788-19623823	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1047513	chr10:19461947-19810770	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv540507	chr10:19461947-19810770	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv948246	chr10:19462519-19465184	Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6481773	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:19438400-19489000	Weak transcription	Fetal Intestine Small	intestine
2	chr10:19457600-19475800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr10:19458200-19465800	Weak transcription	Fetal Intestine Large	intestine

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