Variant report

Variant	rs545
Chromosome Location	chr5:80562120-80562121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80540741..80543266-chr5:80561744..80563838,2	K562	blood:
2	chr5:80559870..80562227-chr5:80563019..80565306,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10036376	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10041063	0.81[CEU][hapmap]
rs10055018	0.89[EUR][1000 genomes]
rs10071174	0.95[EUR][1000 genomes]
rs10073527	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074794	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10078279	0.81[CEU][hapmap]
rs10514215	0.83[ASW][hapmap];0.95[CEU][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10514216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11950033	0.81[CEU][hapmap]
rs11960275	0.83[EUR][1000 genomes]
rs12516414	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13155580	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]
rs13159978	1.00[JPT][hapmap]
rs13170098	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13172928	0.88[EUR][1000 genomes]
rs1566432	0.81[CEU][hapmap]
rs16876403	1.00[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs17294956	0.83[ASW][hapmap];0.95[CEU][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1870061	1.00[JPT][hapmap]
rs2270823	0.81[CEU][hapmap]
rs2270824	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs2277037	0.91[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28819671	0.94[EUR][1000 genomes]
rs2897390	0.81[CEU][hapmap]
rs4703828	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4704707	0.81[CEU][hapmap]
rs4704709	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4704710	0.81[CEU][hapmap]
rs4704717	1.00[CEU][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs57086010	0.87[EUR][1000 genomes]
rs60434474	0.88[EUR][1000 genomes]
rs6872183	0.93[EUR][1000 genomes]
rs6893467	0.81[CEU][hapmap]
rs7448717	0.94[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs750728	0.95[CEU][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7720009	0.81[CEU][hapmap]

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
rs545	CTC-281B15.1	cis	Thyroid	GTEx
rs545	CTD-2248H3.1	cis	lung	GTEx
rs545	CTC-281B15.1	cis	lung	GTEx
rs545	CTC-281B15.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
2	chr5:80531200-80564200	Weak transcription	HepG2	liver
3	chr5:80541800-80564400	Weak transcription	A549	lung
4	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:80544200-80564600	Weak transcription	HSMMtube	muscle
8	chr5:80545400-80565200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:80545800-80564800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:80546600-80564600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:80548800-80568000	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:80549400-80565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:80549400-80565800	Weak transcription	Lung	lung
14	chr5:80550400-80563800	Weak transcription	NHEK	skin
15	chr5:80550400-80564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:80550800-80564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:80551200-80562200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:80551200-80562600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:80551200-80564200	Weak transcription	Fetal Intestine Large	intestine
20	chr5:80551200-80564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:80551200-80565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:80551400-80564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:80552800-80567200	Weak transcription	Brain Anterior Caudate	brain
24	chr5:80553000-80564800	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:80554400-80563600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:80554600-80563800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:80554600-80576400	Weak transcription	Pancreas	Pancrea
28	chr5:80555200-80564600	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:80555200-80564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:80555200-80568600	Weak transcription	Fetal Stomach	stomach
31	chr5:80555600-80562600	Weak transcription	Right Ventricle	heart
32	chr5:80555600-80564000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:80555600-80564800	Weak transcription	Gastric	stomach
34	chr5:80555600-80565600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:80555800-80564200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:80555800-80564800	Weak transcription	Aorta	Aorta
37	chr5:80556000-80565800	Weak transcription	Adipose Nuclei	Adipose
38	chr5:80558000-80564400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:80558200-80568000	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:80558800-80564000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:80558800-80565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:80559200-80563800	Strong transcription	Left Ventricle	heart
43	chr5:80559600-80568400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:80559800-80567200	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:80560000-80566000	Weak transcription	Ovary	ovary
46	chr5:80560200-80562200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:80560200-80562800	Weak transcription	Psoas Muscle	Psoas
48	chr5:80560200-80565800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr5:80560200-80570000	Weak transcription	Primary B cells from cord blood	blood
50	chr5:80560400-80562800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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