Variant report

Variant	rs13155580
Chromosome Location	chr5:80554700-80554701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10036376	0.90[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10055018	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10071174	0.94[EUR][1000 genomes]
rs10073527	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074794	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10514215	0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10514216	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11960275	0.85[EUR][1000 genomes]
rs12516414	0.95[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs13159978	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13170098	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13172928	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16876403	0.94[CEU][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs17228569	0.85[CHB][hapmap]
rs17294956	0.89[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1870061	1.00[JPT][hapmap]
rs2270824	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2277037	0.85[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs28819671	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4703828	0.95[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4704709	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4704717	0.94[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs545	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57086010	0.88[EUR][1000 genomes]
rs60434474	0.88[EUR][1000 genomes]
rs6872183	0.92[EUR][1000 genomes]
rs7448717	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs750728	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[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
rs13155580	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs13155580	CTC-281B15.1	cis	Thyroid	GTEx
rs13155580	CTD-2248H3.1	cis	lung	GTEx
rs13155580	CTC-281B15.1	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
2	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
4	chr5:80531200-80564200	Weak transcription	HepG2	liver
5	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
6	chr5:80532200-80556800	Weak transcription	Dnd41	blood
7	chr5:80539000-80555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:80541800-80564400	Weak transcription	A549	lung
9	chr5:80542200-80557000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:80544000-80557000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:80544200-80561400	Weak transcription	NHLF	lung
15	chr5:80544200-80564600	Weak transcription	HSMMtube	muscle
16	chr5:80545200-80555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:80545400-80565200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:80545800-80564800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:80546600-80556800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:80546600-80564600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:80547600-80555600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:80547800-80555400	Strong transcription	Aorta	Aorta
23	chr5:80548200-80555600	Strong transcription	Fetal Muscle Leg	muscle
24	chr5:80548200-80557600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:80548200-80559400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:80548400-80555600	Strong transcription	Right Ventricle	heart
27	chr5:80548800-80559400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:80548800-80568000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:80549000-80554800	Weak transcription	Brain Angular Gyrus	brain
30	chr5:80549200-80561400	Weak transcription	Liver	Liver
31	chr5:80549200-80562000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:80549400-80565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:80549400-80565800	Weak transcription	Lung	lung
34	chr5:80550200-80560400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:80550400-80554800	Weak transcription	Brain Substantia Nigra	brain
36	chr5:80550400-80563800	Weak transcription	NHEK	skin
37	chr5:80550400-80564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:80550800-80564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:80551000-80554800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:80551000-80555000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:80551000-80557200	Strong transcription	Left Ventricle	heart
42	chr5:80551200-80555000	Weak transcription	Fetal Stomach	stomach
43	chr5:80551200-80562200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:80551200-80562600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:80551200-80564200	Weak transcription	Fetal Intestine Large	intestine
46	chr5:80551200-80564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:80551200-80565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:80551400-80555000	Weak transcription	Fetal Intestine Small	intestine
49	chr5:80551400-80555800	Weak transcription	Spleen	Spleen
50	chr5:80551400-80564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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