Variant report

Variant	rs10078279
Chromosome Location	chr5:80555786-80555787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10036376	0.82[CEU][hapmap]
rs10038684	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.87[CEU][hapmap]
rs1055383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876403	0.81[CEU][hapmap]
rs17294418	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.87[CEU][hapmap]
rs2270823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2897390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365865	0.83[ASN][1000 genomes]
rs68077638	0.83[ASN][1000 genomes]
rs6866499	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6893467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.87[AMR][1000 genomes]
rs7448717	0.84[CEU][hapmap]
rs750728	0.87[CEU][hapmap]
rs7709071	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7709149	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7720009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734902	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs921928	1.00[CHB][hapmap]
rs9293841	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10078279	CTC-281B15.1	cis	Artery Aorta	GTEx
rs10078279	CTD-2248H3.1	cis	lung	GTEx
rs10078279	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs10078279	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs10078279	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs10078279	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs10078279	CTC-281B15.1	cis	Thyroid	GTEx
rs10078279	CTC-281B15.1	cis	lung	GTEx
rs10078279	CKMT2	cis	normal skin	skin_eQTL
rs10078279	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs10078279	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs10078279	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs10078279	CTD-2248H3.1	cis	Thyroid	GTEx
rs10078279	CTC-281B15.1	cis	Stomach	GTEx

Chromatin state (count:69 , 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	chr5:80541800-80564400	Weak transcription	A549	lung
8	chr5:80542200-80557000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:80544000-80557000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:80544200-80561400	Weak transcription	NHLF	lung
14	chr5:80544200-80564600	Weak transcription	HSMMtube	muscle
15	chr5:80545400-80565200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:80545800-80564800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:80546600-80556800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:80546600-80564600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:80548200-80557600	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:80548200-80559400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:80548800-80559400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:80548800-80568000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:80549200-80561400	Weak transcription	Liver	Liver
24	chr5:80549200-80562000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:80549400-80565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:80549400-80565800	Weak transcription	Lung	lung
27	chr5:80550200-80560400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:80550400-80563800	Weak transcription	NHEK	skin
29	chr5:80550400-80564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:80550800-80564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:80551000-80557200	Strong transcription	Left Ventricle	heart
32	chr5:80551200-80562200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:80551200-80562600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:80551200-80564200	Weak transcription	Fetal Intestine Large	intestine
35	chr5:80551200-80564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:80551200-80565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:80551400-80555800	Weak transcription	Spleen	Spleen
38	chr5:80551400-80564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:80551600-80556200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:80551600-80558000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:80552000-80559800	Weak transcription	Primary B cells from cord blood	blood
42	chr5:80552800-80567200	Weak transcription	Brain Anterior Caudate	brain
43	chr5:80553000-80564800	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:80553600-80556000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:80554000-80556000	Strong transcription	Adipose Nuclei	Adipose
46	chr5:80554200-80555800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr5:80554400-80555800	Strong transcription	Primary T cells from cord blood	blood
48	chr5:80554400-80555800	Strong transcription	Ovary	ovary
49	chr5:80554400-80555800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr5:80554400-80563600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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