Variant report

Variant	rs11635080
Chromosome Location	chr15:75878956-75878957
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11636199	0.86[EUR][1000 genomes]
rs12708520	0.86[EUR][1000 genomes]
rs12909863	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13380103	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28623700	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28693593	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28783769	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4075522	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4393535	0.82[EUR][1000 genomes]
rs4886715	0.82[EUR][1000 genomes]
rs4886716	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60972074	0.85[EUR][1000 genomes]
rs62027181	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62027209	0.91[EUR][1000 genomes]
rs7163451	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7163907	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7170787	0.86[EUR][1000 genomes]
rs7184046	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8036884	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9944207	0.82[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
rs11635080	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs11635080	MAN2C1	cis	Artery Aorta	GTEx
rs11635080	MAN2C1	cis	Artery Tibial	GTEx
rs11635080	MAN2C1	cis	Thyroid	GTEx
rs11635080	MAN2C1	cis	Stomach	GTEx
rs11635080	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs11635080	MAN2C1	cis	Esophagus Mucosa	GTEx
rs11635080	MAN2C1	cis	Esophagus Muscularis	GTEx
rs11635080	MAN2C1	cis	Heart Left Ventricle	GTEx
rs11635080	MAN2C1	cis	Nerve Tibial	GTEx
rs11635080	MAN2C1	cis	lung	GTEx
rs11635080	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs11635080	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75872200-75888600	Weak transcription	Aorta	Aorta
2	chr15:75872400-75879800	Weak transcription	Fetal Stomach	stomach
3	chr15:75872400-75882600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:75872400-75882600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:75872400-75882600	Weak transcription	Adipose Nuclei	Adipose
6	chr15:75872400-75882600	Weak transcription	NHDF-Ad	bronchial
7	chr15:75872400-75882800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:75872400-75882800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:75872400-75883000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:75872400-75883600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:75872400-75883600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:75872400-75883600	Weak transcription	Fetal Intestine Large	intestine
13	chr15:75872400-75883800	Weak transcription	Fetal Heart	heart
14	chr15:75872400-75884000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:75872400-75884000	Weak transcription	Spleen	Spleen
16	chr15:75872400-75884000	Weak transcription	NHEK	skin
17	chr15:75872400-75884200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:75872400-75884200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:75872400-75884200	Weak transcription	Left Ventricle	heart
20	chr15:75872400-75884200	Weak transcription	Stomach Mucosa	stomach
21	chr15:75872400-75884200	Weak transcription	GM12878-XiMat	blood
22	chr15:75872400-75885800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:75872400-75886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:75872400-75886000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:75872400-75886600	Weak transcription	Primary B cells from cord blood	blood
26	chr15:75872400-75886600	Weak transcription	Brain Anterior Caudate	brain
27	chr15:75872400-75886600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:75872400-75886600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:75872400-75886600	Weak transcription	NH-A	brain
30	chr15:75872400-75886800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:75872400-75886800	Weak transcription	Fetal Lung	lung
32	chr15:75872400-75887600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:75872400-75887800	Weak transcription	Brain Angular Gyrus	brain
34	chr15:75872400-75887800	Weak transcription	Lung	lung
35	chr15:75872400-75888000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:75872400-75888000	Weak transcription	Brain Substantia Nigra	brain
37	chr15:75872400-75888200	Weak transcription	NHLF	lung
38	chr15:75872400-75888400	Weak transcription	Fetal Kidney	kidney
39	chr15:75872400-75889600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:75872400-75890600	Weak transcription	Psoas Muscle	Psoas
41	chr15:75872400-75891600	Weak transcription	Pancreas	Pancrea
42	chr15:75872400-75892000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:75872400-75898600	Weak transcription	Small Intestine	intestine
44	chr15:75872600-75880200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:75872600-75880800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr15:75872600-75882200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr15:75872600-75882600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:75872600-75882600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:75872600-75882600	Weak transcription	Placenta	Placenta
50	chr15:75872600-75883000	Weak transcription	Fetal Intestine Small	intestine

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