Variant report

Variant	rs13172928
Chromosome Location	chr5:80588572-80588573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10055018	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10071174	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10073527	0.82[EUR][1000 genomes]
rs10074794	0.83[EUR][1000 genomes]
rs10514216	0.88[EUR][1000 genomes]
rs11960275	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12516414	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12652649	0.82[ASN][1000 genomes]
rs13155580	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16876403	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2270824	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2277037	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28819671	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4703828	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4703832	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4703833	0.83[EUR][1000 genomes]
rs4704709	0.82[EUR][1000 genomes]
rs4704717	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs545	0.88[EUR][1000 genomes]
rs57086010	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59563495	0.80[ASN][1000 genomes]
rs60434474	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6871676	0.82[ASN][1000 genomes]
rs6872183	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7448717	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13172928	CTD-2248H3.1	cis	lung	GTEx
rs13172928	CTC-281B15.1	cis	lung	GTEx
rs13172928	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs13172928	CTC-281B15.1	cis	Thyroid	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80572000-80595200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:80578800-80595200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80579800-80589000	Weak transcription	Fetal Heart	heart
4	chr5:80581600-80595800	Weak transcription	Small Intestine	intestine
5	chr5:80584200-80595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:80584400-80595000	Weak transcription	NH-A	brain
7	chr5:80585600-80588600	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:80586400-80595000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:80586400-80595000	Weak transcription	Hela-S3	cervix
10	chr5:80586800-80595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:80587000-80595000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:80587000-80595000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:80587200-80588600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr5:80587400-80589000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:80587400-80589600	ZNF genes & repeats	Fetal Lung	lung
16	chr5:80587400-80590200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:80587600-80588600	ZNF genes & repeats	Liver	Liver
18	chr5:80587600-80589800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr5:80587600-80591400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:80587800-80589600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr5:80588000-80588800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:80588000-80589000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:80588000-80589000	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr5:80588000-80589600	ZNF genes & repeats	Fetal Kidney	kidney
25	chr5:80588000-80595000	Weak transcription	Osteobl	bone
26	chr5:80588000-80595200	Weak transcription	A549	lung
27	chr5:80588200-80588600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr5:80588200-80589000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:80588200-80594600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:80588200-80594600	Weak transcription	Ovary	ovary
31	chr5:80588200-80595000	Weak transcription	NHLF	lung
32	chr5:80588200-80595200	Weak transcription	Right Atrium	heart
33	chr5:80588200-80596400	Weak transcription	Right Ventricle	heart
34	chr5:80588400-80588600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:80588400-80588800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:80588400-80593000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:80588400-80593800	Weak transcription	HSMMtube	muscle
38	chr5:80588400-80595000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:80588400-80595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:80588400-80595200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:80588400-80595200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr5:80588400-80595200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:80588400-80595800	Weak transcription	Left Ventricle	heart
44	chr5:80588400-80596400	Weak transcription	Psoas Muscle	Psoas

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