Variant report

Variant	rs5745920
Chromosome Location	chr15:75645350-75645351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75644367-75645445	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:75644216-75645394	K562	blood:	n/a	n/a
3	POLR2A	chr15:75645300-75645458	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:75639141-75646939	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
NEIL1	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10152155	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10220738	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775209	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072542	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631052	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11634863	0.85[EUR][1000 genomes]
rs11636031	0.82[EUR][1000 genomes]
rs11637068	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637586	0.81[EUR][1000 genomes]
rs12708518	0.81[EUR][1000 genomes]
rs12708519	0.82[EUR][1000 genomes]
rs12916964	0.81[EUR][1000 genomes]
rs28610581	0.82[EUR][1000 genomes]
rs28737338	0.82[EUR][1000 genomes]
rs3809547	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4243033	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4297648	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4299117	0.81[EUR][1000 genomes]
rs4322627	0.82[EUR][1000 genomes]
rs4368141	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4451914	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4462560	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4486847	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4545784	0.84[EUR][1000 genomes]
rs4564532	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886443	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886446	0.82[EUR][1000 genomes]
rs4886699	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886700	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4886703	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4886707	0.84[EUR][1000 genomes]
rs4886708	0.84[EUR][1000 genomes]
rs4886712	0.81[EUR][1000 genomes]
rs6495182	0.82[EUR][1000 genomes]
rs7166737	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7171507	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175852	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7176938	0.81[EUR][1000 genomes]
rs7180574	0.82[EUR][1000 genomes]
rs7402293	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7402844	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7495610	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8023268	0.82[EUR][1000 genomes]
rs8023815	0.82[EUR][1000 genomes]
rs8024244	0.82[EUR][1000 genomes]
rs8028182	0.88[AFR][1000 genomes]
rs8028277	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8029112	0.82[EUR][1000 genomes]
rs8029394	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8030802	0.82[EUR][1000 genomes]
rs8034317	0.83[EUR][1000 genomes]
rs8036758	0.82[EUR][1000 genomes]
rs8038760	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
6	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
8	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
9	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs5745920	MAN2C1	cis	Whole Blood	GTEx
rs5745920	MAN2C1	cis	Heart Left Ventricle	GTEx
rs5745920	MAN2C1	cis	Esophagus Muscularis	GTEx
rs5745920	MAN2C1	cis	lung	GTEx
rs5745920	MAN2C1	cis	Artery Aorta	GTEx
rs5745920	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs5745920	MAN2C1	cis	Nerve Tibial	GTEx
rs5745920	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs5745920	MAN2C1	cis	Esophagus Mucosa	GTEx
rs5745920	MAN2C1	cis	Thyroid	GTEx
rs5745920	MAN2C1	cis	Stomach	GTEx
rs5745920	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs5745920	MAN2C1	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75641200-75646800	Weak transcription	Aorta	Aorta
2	chr15:75641200-75655000	Weak transcription	K562	blood
3	chr15:75641400-75645600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:75641400-75646800	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:75641400-75646800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:75641400-75647200	Weak transcription	Brain Anterior Caudate	brain
7	chr15:75641400-75647400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:75641400-75647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:75641400-75647800	Weak transcription	Ovary	ovary
10	chr15:75641400-75648200	Weak transcription	Psoas Muscle	Psoas
11	chr15:75641400-75651200	Weak transcription	HSMM	muscle
12	chr15:75641400-75655400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:75641400-75658600	Weak transcription	HUVEC	blood vessel
14	chr15:75641600-75645800	Weak transcription	HepG2	liver
15	chr15:75641600-75647000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:75641600-75647200	Weak transcription	Brain Angular Gyrus	brain
17	chr15:75641600-75647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:75641600-75647400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:75641600-75647400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:75641600-75647800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:75641600-75648200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:75641600-75648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:75641600-75648400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:75641600-75648400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:75641600-75648800	Weak transcription	Fetal Lung	lung
26	chr15:75641600-75650400	Weak transcription	Brain Substantia Nigra	brain
27	chr15:75641600-75654200	Weak transcription	Small Intestine	intestine
28	chr15:75641600-75659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:75641600-75659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:75641800-75645800	Weak transcription	Fetal Intestine Large	intestine
31	chr15:75641800-75646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:75641800-75646000	Weak transcription	Esophagus	oesophagus
33	chr15:75641800-75646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:75641800-75646200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:75641800-75646200	Weak transcription	NHEK	skin
36	chr15:75641800-75646600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:75641800-75647200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:75641800-75647400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:75641800-75647400	Weak transcription	Hela-S3	cervix
40	chr15:75641800-75648200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:75641800-75648800	Weak transcription	HMEC	breast
42	chr15:75641800-75651400	Weak transcription	Stomach Mucosa	stomach
43	chr15:75641800-75659600	Weak transcription	Fetal Heart	heart
44	chr15:75642000-75659600	Strong transcription	Fetal Intestine Small	intestine
45	chr15:75642200-75659800	Weak transcription	Fetal Brain Male	brain
46	chr15:75642400-75649000	Weak transcription	Osteobl	bone
47	chr15:75642400-75659800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:75642600-75646000	Weak transcription	Primary T cells from cord blood	blood
49	chr15:75642600-75646000	Weak transcription	Brain Germinal Matrix	brain
50	chr15:75642600-75646000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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