Variant report

Variant	rs750728
Chromosome Location	chr5:80529756-80529757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10041063	0.85[CEU][hapmap]
rs10073527	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10074794	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10078279	0.87[CEU][hapmap]
rs10514213	0.81[CEU][hapmap]
rs10514215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10514216	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1055383	0.84[CEU][hapmap]
rs11950033	0.85[CEU][hapmap]
rs11960275	0.81[EUR][1000 genomes]
rs12516414	0.95[CEU][hapmap]
rs13155580	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13170098	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13184427	1.00[JPT][hapmap]
rs1566432	0.85[CEU][hapmap]
rs16876403	0.95[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs16878572	1.00[JPT][hapmap]
rs17294418	0.81[CEU][hapmap]
rs17294956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270823	0.85[CEU][hapmap]
rs2270824	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs2270825	1.00[JPT][hapmap]
rs2277037	0.86[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2897389	0.80[CEU][hapmap]
rs2897390	0.85[CEU][hapmap]
rs4703827	0.81[CEU][hapmap]
rs4703828	0.95[CEU][hapmap]
rs4704707	0.85[CEU][hapmap]
rs4704709	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	0.85[CEU][hapmap]
rs4704717	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs545	0.95[CEU][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57086010	0.84[EUR][1000 genomes]
rs60434474	0.83[EUR][1000 genomes]
rs6859306	1.00[JPT][hapmap]
rs6893467	0.85[CEU][hapmap]
rs6899067	1.00[JPT][hapmap]
rs7448717	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7720009	0.85[CEU][hapmap]
rs7725743	1.00[JPT][hapmap]
rs9293841	0.81[CEU][hapmap]
rs976741	1.00[JPT][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs750728	CTC-281B15.1	cis	lung	GTEx
rs750728	CTC-281B15.1	cis	Stomach	GTEx
rs750728	CTD-2248H3.1	cis	lung	GTEx
rs750728	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs750728	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs750728	CTC-281B15.1	cis	Thyroid	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80491200-80530000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:80498800-80530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:80506000-80530000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:80509400-80530000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:80520600-80530200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr5:80522400-80530000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:80522600-80530400	Weak transcription	Primary T cells from cord blood	blood
8	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:80527000-80530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
13	chr5:80528200-80531000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:80528200-80531800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr5:80528400-80530000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:80528400-80530000	Active TSS	Right Atrium	heart
17	chr5:80528400-80531600	Enhancers	Spleen	Spleen
18	chr5:80528600-80530000	Active TSS	Psoas Muscle	Psoas
19	chr5:80528600-80530400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr5:80528600-80531400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr5:80528600-80531600	Enhancers	Fetal Thymus	thymus
22	chr5:80528600-80532000	Enhancers	Lung	lung
23	chr5:80528800-80529800	Enhancers	Liver	Liver
24	chr5:80528800-80529800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr5:80528800-80531000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:80528800-80531400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:80528800-80531400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr5:80529000-80529800	Active TSS	Ovary	ovary
29	chr5:80529000-80530000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:80529000-80530000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr5:80529000-80530000	Active TSS	Fetal Heart	heart
32	chr5:80529000-80530800	Active TSS	Left Ventricle	heart
33	chr5:80529400-80529800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr5:80529400-80529800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr5:80529400-80529800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr5:80529400-80529800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:80529400-80529800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:80529400-80529800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:80529400-80529800	Active TSS	Brain Hippocampus Middle	brain
40	chr5:80529400-80529800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:80529400-80530000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:80529400-80530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:80529400-80530000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:80529400-80530000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:80529400-80530000	Active TSS	Fetal Muscle Trunk	muscle
46	chr5:80529400-80530000	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr5:80529400-80530400	Weak transcription	Pancreas	Pancrea
48	chr5:80529400-80530400	Weak transcription	Thymus	Thymus
49	chr5:80529400-80530600	Weak transcription	Esophagus	oesophagus
50	chr5:80529400-80531400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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