Variant report

Variant	rs4235106
Chromosome Location	chr4:69887437-69887438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UGT2A3-9	chr4:69887374-69888058	NONHSAT096750

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10006595	0.90[EUR][1000 genomes]
rs10012215	0.80[ASN][1000 genomes]
rs10012607	0.81[ASN][1000 genomes]
rs10019619	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10021748	0.82[CHB][hapmap]
rs10030220	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11249520	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725519	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12501837	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12509175	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12512098	0.91[EUR][1000 genomes]
rs12648830	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs13102620	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13108709	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13116752	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13127081	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13128177	0.87[EUR][1000 genomes]
rs13140844	0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13145165	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13145304	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147569	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13147648	0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1458230	0.81[EUR][1000 genomes]
rs1841055	0.92[EUR][1000 genomes]
rs1902923	0.87[EUR][1000 genomes]
rs1902929	0.90[CHB][hapmap]
rs2011000	0.84[EUR][1000 genomes]
rs2292524	0.80[AMR][1000 genomes]
rs2331627	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28386872	0.94[EUR][1000 genomes]
rs28485675	0.81[EUR][1000 genomes]
rs3922514	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4235108	0.90[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4235111	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235112	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4299665	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4299666	0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4304032	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4305590	0.90[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4312824	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4351079	0.81[ASN][1000 genomes]
rs4353969	0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4365792	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4377650	0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4400060	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4400061	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4413468	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs4422474	0.84[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4440295	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4446390	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4495114	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4518318	0.80[ASN][1000 genomes]
rs4576082	0.89[CHB][hapmap]
rs4591680	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4600986	0.91[CHB][hapmap]
rs4607293	0.81[ASN][1000 genomes]
rs4694490	0.91[EUR][1000 genomes]
rs4694491	0.92[EUR][1000 genomes]
rs4694551	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694588	0.81[ASN][1000 genomes]
rs4694610	0.83[CHB][hapmap]
rs6422321	0.81[ASN][1000 genomes]
rs6827511	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6828317	0.91[EUR][1000 genomes]
rs6831147	0.85[EUR][1000 genomes]
rs6837000	0.86[EUR][1000 genomes]
rs6839405	0.87[EUR][1000 genomes]
rs6843788	0.91[EUR][1000 genomes]
rs7435274	0.80[ASN][1000 genomes]
rs7438033	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7438808	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7441736	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7442486	0.80[CHB][hapmap]
rs7657426	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs7662632	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7673174	0.89[EUR][1000 genomes]
rs7691258	0.89[EUR][1000 genomes]
rs7691445	0.89[EUR][1000 genomes]
rs988887	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005513	chr4:69446718-69890307	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv829962	chr4:69786869-69910283	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv2757064	chr4:69863174-69901607	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv980213	chr4:69870183-69893292	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69886000-69889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:69886000-69889800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:69886000-69891000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:69886200-69889200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:69886200-69889400	Enhancers	Liver	Liver
6	chr4:69886200-69889800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:69886200-69893000	Enhancers	HepG2	liver
8	chr4:69887200-69890800	Weak transcription	Fetal Intestine Large	intestine
9	chr4:69887400-69891200	Weak transcription	A549	lung

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