Variant report

Variant	rs3898713
Chromosome Location	chr5:59053490-59053491
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10043265	0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs10043283	0.83[CHB][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs10514857	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs10940649	1.00[YRI][hapmap]
rs11949859	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11951422	1.00[MKK][hapmap]
rs12152908	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12187752	0.83[CHB][hapmap];0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs12188131	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13155799	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs1362941	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1362942	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437124	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs1504982	0.91[ASN][1000 genomes]
rs1504984	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16877195	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17310599	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17311853	1.00[YRI][hapmap]
rs17311925	1.00[YRI][hapmap]
rs17369708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17371174	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17381667	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[ASN][1000 genomes]
rs17381695	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17381723	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17382202	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17440909	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17441217	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17441825	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17742120	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17742544	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743216	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17799161	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017574	0.81[ASN][1000 genomes]
rs2164660	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583502	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4577665	0.91[ASN][1000 genomes]
rs4699942	0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs4699943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700340	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700341	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs55704150	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55868825	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56199003	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56312915	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6450528	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs6450530	0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[ASN][1000 genomes]
rs6860907	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[ASN][1000 genomes]
rs6874708	0.90[ASN][1000 genomes]
rs6889294	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs6897073	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751211	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72751218	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72751224	0.83[EUR][1000 genomes]
rs72751226	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72751229	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751231	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751232	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751233	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751234	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751235	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751237	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751241	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751244	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751247	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751250	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72751252	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751264	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72751266	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs756211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs756212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7703963	1.00[YRI][hapmap]
rs7708952	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs7710199	0.90[ASN][1000 genomes]
rs7736817	0.83[CHB][hapmap];0.81[CHD][hapmap];0.89[ASN][1000 genomes]
rs877745	0.83[CHB][hapmap];0.85[CHD][hapmap];0.91[ASN][1000 genomes]
rs981230	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs986400	1.00[MKK][hapmap]

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	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59039400-59059800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59042600-59055400	Weak transcription	Esophagus	oesophagus
3	chr5:59047600-59055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:59048000-59055200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:59048800-59053800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:59048800-59059400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:59048800-59064000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:59049000-59055600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:59051600-59055400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:59051800-59055200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:59052200-59053600	Enhancers	HepG2	liver
12	chr5:59052200-59054400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:59052400-59054800	Enhancers	Colon Smooth Muscle	Colon
14	chr5:59052400-59056000	Enhancers	Stomach Mucosa	stomach
15	chr5:59052400-59056600	Enhancers	HMEC	breast
16	chr5:59052600-59053800	Weak transcription	NHEK	skin
17	chr5:59052600-59064200	Weak transcription	Aorta	Aorta
18	chr5:59052800-59056000	Flanking Active TSS	A549	lung
19	chr5:59052800-59057600	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr5:59053000-59055400	Genic enhancers	Hela-S3	cervix
21	chr5:59053200-59053800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:59053200-59054200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr5:59053200-59055400	Weak transcription	Fetal Kidney	kidney
24	chr5:59053200-59058800	Weak transcription	Fetal Intestine Large	intestine
25	chr5:59053400-59053600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:59053400-59054200	Enhancers	Small Intestine	intestine
27	chr5:59053400-59055400	Enhancers	HUVEC	blood vessel

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