Variant report

Variant	rs7728465
Chromosome Location	chr5:80534139-80534140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:80527933..80529757-chr5:80532503..80536137,3	K562	blood:
2	chr5:80533835..80535952-chr5:80536358..80538969,2	K562	blood:
3	chr5:80533844..80536662-chr5:80539256..80543290,4	K562	blood:

Variant related genes	Relation type
ENSG00000131730	Chromatin interaction
ENSG00000248794	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10038684	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10041063	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053706	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10055063	0.80[AMR][1000 genomes]
rs10066296	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10078279	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10474656	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514213	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055383	0.91[AMR][1000 genomes]
rs10942945	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950033	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13362314	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1566432	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294418	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270823	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28464111	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650401	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897389	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897390	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703827	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704707	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704708	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704710	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704712	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704715	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704720	0.92[AMR][1000 genomes]
rs59132806	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60488995	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60904680	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61244991	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866499	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6893467	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73130869	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381116	0.84[AMR][1000 genomes]
rs7720009	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9293841	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7728465	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs7728465	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs7728465	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs7728465	CTD-2248H3.1	cis	Thyroid	GTEx
rs7728465	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs7728465	CTC-281B15.1	cis	lung	GTEx
rs7728465	CTC-281B15.1	cis	Artery Aorta	GTEx
rs7728465	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs7728465	CTC-281B15.1	cis	Stomach	GTEx
rs7728465	CTC-281B15.1	cis	Thyroid	GTEx
rs7728465	CTD-2248H3.1	cis	lung	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
3	chr5:80529400-80535200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:80529400-80543400	Weak transcription	NHLF	lung
7	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:80529600-80535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
11	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:80530000-80537200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:80530200-80541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:80530600-80537400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:80530600-80542800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:80530600-80543000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:80530600-80543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:80530600-80544000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:80531000-80540200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:80531200-80536800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:80531200-80538600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:80531200-80540000	Weak transcription	Aorta	Aorta
27	chr5:80531200-80542400	Weak transcription	Primary T cells from cord blood	blood
28	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
30	chr5:80531200-80564200	Weak transcription	HepG2	liver
31	chr5:80531400-80536000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:80531400-80538200	Weak transcription	Pancreas	Pancrea
33	chr5:80531600-80536000	Weak transcription	Spleen	Spleen
34	chr5:80531600-80542800	Weak transcription	Brain Germinal Matrix	brain
35	chr5:80531800-80534600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:80531800-80535400	Weak transcription	Fetal Brain Male	brain
37	chr5:80531800-80536000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:80531800-80538200	Weak transcription	HSMMtube	muscle
39	chr5:80531800-80541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:80531800-80543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
42	chr5:80532000-80534600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:80532000-80534800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:80532000-80535400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:80532000-80538800	Weak transcription	Gastric	stomach
46	chr5:80532000-80540800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr5:80532000-80541600	Weak transcription	Fetal Brain Female	brain
48	chr5:80532000-80542600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:80532000-80548400	Weak transcription	Lung	lung
50	chr5:80532200-80534400	Weak transcription	Stomach Smooth Muscle	stomach

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