Variant report

Variant	rs62027209
Chromosome Location	chr15:75871626-75871627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75743800..75745854-chr15:75871441..75873983,2	K562	blood:
2	chr15:75741711..75746813-chr15:75868980..75872679,7	MCF-7	breast:
3	chr15:75651898..75654769-chr15:75870111..75872338,3	MCF-7	breast:
4	chr15:75746665..75750304-chr15:75867936..75873114,8	K562	blood:
5	chr15:75870263..75872383-chr15:75940426..75942164,2	K562	blood:
6	chr15:75870545..75872702-chr15:75967179..75968933,2	K562	blood:
7	chr15:75741664..75745730-chr15:75869940..75872786,3	MCF-7	breast:
8	chr15:75744354..75750304-chr15:75868474..75873810,11	K562	blood:
9	chr15:75868548..75873773-chr15:75928671..75933652,6	K562	blood:
10	chr15:75868548..75873380-chr15:75928279..75933652,7	K562	blood:
11	chr15:75869706..75871837-chr15:75939750..75941474,2	MCF-7	breast:
12	chr15:75869532..75872781-chr15:75929534..75934767,14	MCF-7	breast:
13	chr15:75658017..75661976-chr15:75870089..75873800,4	K562	blood:
14	chr15:75658017..75660479-chr15:75870000..75872676,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173548	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000260892	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000260206	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs11635080	0.91[EUR][1000 genomes]
rs11636031	0.81[EUR][1000 genomes]
rs11636199	0.88[EUR][1000 genomes]
rs12708519	0.81[EUR][1000 genomes]
rs12708520	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12909863	0.88[EUR][1000 genomes]
rs13380103	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs28610581	0.81[EUR][1000 genomes]
rs28623700	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs28693593	0.90[EUR][1000 genomes]
rs28783769	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4075522	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4322627	0.81[EUR][1000 genomes]
rs4393535	0.84[EUR][1000 genomes]
rs4886715	0.84[EUR][1000 genomes]
rs4886716	0.89[EUR][1000 genomes]
rs4886722	0.81[EUR][1000 genomes]
rs60972074	0.87[EUR][1000 genomes]
rs62027181	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6495182	0.81[EUR][1000 genomes]
rs7163451	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7163907	0.87[EUR][1000 genomes]
rs7170787	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7175223	0.80[EUR][1000 genomes]
rs7180574	0.81[EUR][1000 genomes]
rs7184046	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8023268	0.81[EUR][1000 genomes]
rs8023815	0.81[EUR][1000 genomes]
rs8024244	0.81[EUR][1000 genomes]
rs8029112	0.81[EUR][1000 genomes]
rs8030802	0.81[EUR][1000 genomes]
rs8036758	0.81[EUR][1000 genomes]
rs8036884	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8037089	0.80[EUR][1000 genomes]
rs9920028	0.81[EUR][1000 genomes]
rs9944207	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs62027209	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs62027209	MAN2C1	cis	Stomach	GTEx
rs62027209	MAN2C1	cis	Thyroid	GTEx
rs62027209	MAN2C1	cis	Artery Aorta	GTEx
rs62027209	MAN2C1	cis	Nerve Tibial	GTEx
rs62027209	MAN2C1	cis	Esophagus Muscularis	GTEx
rs62027209	MAN2C1	cis	Esophagus Mucosa	GTEx
rs62027209	MAN2C1	cis	lung	GTEx
rs62027209	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs62027209	MAN2C1	cis	Artery Tibial	GTEx
rs62027209	MAN2C1	cis	Whole Blood	GTEx
rs62027209	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs62027209	MAN2C1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75868800-75872400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:75869000-75872000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:75869200-75872000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr15:75869200-75872000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:75869200-75872000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:75869200-75872000	Active TSS	GM12878-XiMat	blood
7	chr15:75869400-75872000	Active TSS	Brain Cingulate Gyrus	brain
8	chr15:75869400-75872000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr15:75869400-75872000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:75869400-75872200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr15:75869400-75872400	Active TSS	NHLF	lung
12	chr15:75869600-75872000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:75869600-75872000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:75869600-75872000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:75869600-75872000	Active TSS	Colonic Mucosa	Colon
16	chr15:75869600-75872000	Active TSS	Fetal Brain Male	brain
17	chr15:75869600-75872000	Active TSS	Fetal Intestine Large	intestine
18	chr15:75869600-75872000	Active TSS	Fetal Stomach	stomach
19	chr15:75869600-75872000	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:75869600-75872200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:75869600-75872200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:75869600-75872200	Active TSS	Ovary	ovary
23	chr15:75869600-75872400	Active TSS	Fetal Kidney	kidney
24	chr15:75869600-75872400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr15:75869800-75872000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr15:75869800-75872000	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr15:75869800-75872000	Active TSS	Muscle Satellite Cultured Cells	--
28	chr15:75869800-75872000	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr15:75869800-75872000	Active TSS	Duodenum Mucosa	Duodenum
30	chr15:75869800-75872000	Active TSS	Fetal Muscle Trunk	muscle
31	chr15:75869800-75872000	Active TSS	Left Ventricle	heart
32	chr15:75869800-75872000	Active TSS	A549	lung
33	chr15:75869800-75872000	Active TSS	NHDF-Ad	bronchial
34	chr15:75869800-75872200	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr15:75869800-75872200	Active TSS	Aorta	Aorta
36	chr15:75869800-75872200	Active TSS	Small Intestine	intestine
37	chr15:75869800-75872400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr15:75869800-75872400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:75869800-75872400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:75869800-75872400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr15:75869800-75872400	Active TSS	Psoas Muscle	Psoas
42	chr15:75869800-75872400	Active TSS	Right Ventricle	heart
43	chr15:75869800-75872400	Active TSS	HSMM	muscle
44	chr15:75869800-75872600	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:75870000-75871800	Active TSS	K562	blood
46	chr15:75870000-75872000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:75870000-75872000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:75870000-75872000	Active TSS	Brain Anterior Caudate	brain
49	chr15:75870000-75872000	Active TSS	Brain Hippocampus Middle	brain
50	chr15:75870000-75872000	Active TSS	Fetal Lung	lung

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