Variant report

Variant	rs16898412
Chromosome Location	chr5:29001077-29001078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10057056	0.93[ASN][1000 genomes]
rs10461852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1587623	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1587627	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16874344	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898181	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16898182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16898405	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16898408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16898409	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898411	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16898418	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898427	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16898430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16898545	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16898551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16898552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs170257	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17617368	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1818122	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs182611	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs184349	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs188783	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2173972	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs221519	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2554912	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs312653	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs312654	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs312655	0.93[ASN][1000 genomes]
rs312657	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs312659	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs312663	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs312664	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs312665	0.81[ASN][1000 genomes]
rs312668	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs312669	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs312672	0.81[ASN][1000 genomes]
rs314785	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs314795	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314796	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314797	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314799	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314800	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314802	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314803	0.95[ASN][1000 genomes]
rs314804	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314813	0.95[ASN][1000 genomes]
rs314817	0.95[ASN][1000 genomes]
rs314820	0.86[ASN][1000 genomes]
rs314822	0.95[ASN][1000 genomes]
rs314825	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs314826	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs314827	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs314834	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs314851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs3792899	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs413031	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs455448	0.95[ASN][1000 genomes]
rs457561	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs463497	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60041854	0.98[ASN][1000 genomes]
rs66698	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66701	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs694336	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs923628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029219	chr5:28370908-29086506	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv537710	chr5:28370908-29086506	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv881649	chr5:28786844-29007308	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv881344	chr5:28786844-29017460	Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv880855	chr5:28786844-29129027	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881674	chr5:28806256-29007308	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv880318	chr5:28806256-29017460	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv880410	chr5:28806256-29017460	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv830243	chr5:28884069-29062804	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1023990	chr5:28917253-29220447	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv597750	chr5:28936053-29145655	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1024307	chr5:28936195-29145676	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1027037	chr5:28936195-29147837	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv597751	chr5:28941373-29144972	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1015334	chr5:28951390-29139719	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv537711	chr5:28951390-29139719	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv523085	chr5:28955799-29145655	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv880921	chr5:28959648-29129027	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv1015344	chr5:28986059-29062414	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv3331594	chr5:28990244-29005934	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1028333	chr5:29000893-29030920	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:28999000-29002200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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