Variant report

Variant	rs6450530
Chromosome Location	chr5:59059508-59059509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65268788..65269336-chr5:59059488..59060259,2	Hela-S3	cervix:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10043265	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs10043283	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs1027747	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10514857	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11949859	0.84[ASN][1000 genomes]
rs12187752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12188131	0.88[ASN][1000 genomes]
rs13155799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168347	0.90[EUR][1000 genomes]
rs1362941	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs1362942	0.88[ASN][1000 genomes]
rs1437124	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1504982	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504984	0.90[ASN][1000 genomes]
rs16877195	0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs17369708	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs17381667	0.83[CHB][hapmap]
rs17381695	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs17381723	0.81[ASN][1000 genomes]
rs17382202	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs17440909	0.83[CHB][hapmap]
rs17441217	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs17441825	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs17742120	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs17742544	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs17743216	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs17799161	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs2164660	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs28583502	0.93[ASN][1000 genomes]
rs2938780	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2938783	0.86[GIH][hapmap]
rs2963826	0.96[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs298063	0.82[TSI][hapmap]
rs298084	0.82[TSI][hapmap]
rs298091	0.84[TSI][hapmap]
rs36143327	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3898713	0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[ASN][1000 genomes]
rs4577665	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699943	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs4700340	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs4700341	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4700342	0.88[EUR][1000 genomes]
rs55704150	0.93[ASN][1000 genomes]
rs55868825	0.88[ASN][1000 genomes]
rs56199003	0.88[ASN][1000 genomes]
rs6450528	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6860907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874708	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6889294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6897073	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[ASN][1000 genomes]
rs72751211	0.84[ASN][1000 genomes]
rs72751218	0.84[ASN][1000 genomes]
rs72751226	0.85[ASN][1000 genomes]
rs72751229	0.88[ASN][1000 genomes]
rs72751231	0.88[ASN][1000 genomes]
rs72751232	0.88[ASN][1000 genomes]
rs72751233	0.88[ASN][1000 genomes]
rs72751234	0.88[ASN][1000 genomes]
rs72751235	0.88[ASN][1000 genomes]
rs72751237	0.88[ASN][1000 genomes]
rs72751241	0.88[ASN][1000 genomes]
rs72751244	0.88[ASN][1000 genomes]
rs72751247	0.88[ASN][1000 genomes]
rs72751250	0.88[ASN][1000 genomes]
rs72751252	0.91[ASN][1000 genomes]
rs72751264	0.88[ASN][1000 genomes]
rs756211	0.82[CHB][hapmap];0.93[ASN][1000 genomes]
rs756212	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs7708952	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710199	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7736817	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs877745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981230	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3449802	chr5:59057795-59059743	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:35 , 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	chr5:59048800-59064000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:59052600-59064200	Weak transcription	Aorta	Aorta
4	chr5:59054200-59062200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:59054600-59061400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:59055200-59061400	Weak transcription	Fetal Brain Male	brain
7	chr5:59055800-59061400	Weak transcription	Esophagus	oesophagus
8	chr5:59055800-59061800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:59055800-59062000	Weak transcription	Fetal Stomach	stomach
10	chr5:59055800-59063600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:59056800-59059600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:59056800-59062200	Weak transcription	HSMM	muscle
13	chr5:59057000-59061400	Weak transcription	Fetal Kidney	kidney
14	chr5:59057000-59062000	Weak transcription	Stomach Mucosa	stomach
15	chr5:59057200-59059600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:59057600-59059800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:59057600-59061200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:59057600-59061800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:59057600-59062000	Weak transcription	Small Intestine	intestine
20	chr5:59057600-59062200	Weak transcription	Fetal Intestine Small	intestine
21	chr5:59057600-59062400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:59057600-59062400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:59057800-59061600	Weak transcription	HMEC	breast
24	chr5:59057800-59062200	Weak transcription	NH-A	brain
25	chr5:59058000-59059600	Weak transcription	Fetal Lung	lung
26	chr5:59058600-59061400	Enhancers	HUVEC	blood vessel
27	chr5:59059200-59060000	Enhancers	NHEK	skin
28	chr5:59059400-59059600	Flanking Active TSS	A549	lung
29	chr5:59059400-59059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:59059400-59059800	Enhancers	Brain Germinal Matrix	brain
31	chr5:59059400-59060000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:59059400-59060000	Enhancers	Colon Smooth Muscle	Colon
33	chr5:59059400-59060200	Flanking Active TSS	Hela-S3	cervix
34	chr5:59059400-59061400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:59059400-59062000	Enhancers	Primary B cells from peripheral blood	blood

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