Variant report

Variant	rs1862629
Chromosome Location	chr5:42824857-42824858
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1074263	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10941591	0.87[ASN][1000 genomes]
rs10941592	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10941593	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12517008	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12519532	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12521615	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13167366	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1345824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345825	0.94[ASN][1000 genomes]
rs1423650	0.83[AMR][1000 genomes]
rs1423653	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423656	0.88[ASN][1000 genomes]
rs1593071	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1833906	0.83[AMR][1000 genomes]
rs1862628	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1862630	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1895457	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014958	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113088	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs230807	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs230812	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230813	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230814	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230816	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs230819	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs230820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2459629	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910851	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910855	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910856	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910862	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910864	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2910871	0.94[ASN][1000 genomes]
rs2910875	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2910880	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2910881	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972756	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972757	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972758	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972759	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972761	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972763	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972767	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972783	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2972992	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2972994	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2972998	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972999	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973000	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973001	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973006	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973011	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2973018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973023	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973028	0.96[ASN][1000 genomes]
rs2973029	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973031	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34417548	0.89[EUR][1000 genomes]
rs34443829	0.88[ASN][1000 genomes]
rs34926728	0.88[ASN][1000 genomes]
rs35293842	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4409101	0.83[AMR][1000 genomes]
rs4866800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4866801	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4866802	0.88[ASN][1000 genomes]
rs4866968	0.83[AMR][1000 genomes]
rs6179	0.86[LWK][hapmap]
rs6180	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62370950	0.88[ASN][1000 genomes]
rs62370952	0.88[ASN][1000 genomes]
rs62370955	0.88[ASN][1000 genomes]
rs6882333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs719756	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs722677	0.85[EUR][1000 genomes]
rs7443044	0.82[AMR][1000 genomes]
rs9637794	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
15	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
16	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42817000-42827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:42821400-42826000	Weak transcription	Fetal Stomach	stomach
3	chr5:42822800-42825800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:42823200-42826400	Enhancers	Fetal Intestine Small	intestine
5	chr5:42823400-42826200	Flanking Active TSS	Liver	Liver
6	chr5:42823400-42826400	Flanking Active TSS	HepG2	liver
7	chr5:42823600-42826200	Enhancers	Fetal Intestine Large	intestine
8	chr5:42824200-42826200	Enhancers	Gastric	stomach
9	chr5:42824200-42826400	Enhancers	Pancreas	Pancrea
10	chr5:42824400-42825000	Enhancers	Adipose Nuclei	Adipose
11	chr5:42824800-42827800	Weak transcription	Rectal Mucosa Donor 31	rectum

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