Variant report

Variant	rs13380103
Chromosome Location	chr15:75875924-75875925
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	ZNF384	chr15:75875824-75875975	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75875350..75877314-chr15:75930301..75933230,3	MCF-7	breast:
2	chr15:75869495..75873752-chr15:75874233..75877262,7	MCF-7	breast:

Variant related genes	Relation type
PTPN9	TF binding region
ENSG00000169410	Chromatin interaction
ENSG00000177971	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10851882	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11632105	0.83[CHB][hapmap]
rs11632813	0.83[CHB][hapmap]
rs11635080	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636031	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs11636199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637586	0.83[EUR][1000 genomes]
rs11638974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11855087	0.83[CHB][hapmap]
rs12324230	0.83[CHB][hapmap]
rs12708518	0.83[EUR][1000 genomes]
rs12708519	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs12708520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909863	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910672	0.84[EUR][1000 genomes]
rs12916256	0.85[ASN][1000 genomes]
rs12916964	0.83[EUR][1000 genomes]
rs13737	0.89[CEU][hapmap]
rs28610581	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs28623700	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28693593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28737338	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28783769	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4075522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4299117	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4322627	0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs4393535	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4430707	0.83[CHB][hapmap]
rs4451914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs4545784	1.00[CEU][hapmap]
rs4564532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs4886443	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs4886446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs4886702	0.83[CHB][hapmap]
rs4886703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs4886704	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4886705	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4886706	0.83[CHB][hapmap]
rs4886707	1.00[CEU][hapmap]
rs4886708	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs4886712	0.83[EUR][1000 genomes]
rs4886715	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4886716	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886722	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs60972074	0.89[EUR][1000 genomes]
rs62027181	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62027209	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6495174	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6495176	0.83[CHB][hapmap]
rs6495181	0.83[CHB][hapmap]
rs6495182	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7162532	0.83[AMR][1000 genomes]
rs7163451	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7163907	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7164541	0.83[CHB][hapmap]
rs7166281	0.88[CEU][hapmap]
rs7166737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs7170787	0.92[EUR][1000 genomes]
rs7175223	0.83[EUR][1000 genomes]
rs7175852	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs7176938	0.83[EUR][1000 genomes]
rs7176989	0.80[ASN][1000 genomes]
rs7180574	0.84[EUR][1000 genomes]
rs7184046	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7495610	0.83[EUR][1000 genomes]
rs8023268	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs8023815	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs8024244	0.84[EUR][1000 genomes]
rs8028182	0.96[YRI][hapmap]
rs8028277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs8029112	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs8030802	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs8034317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8036758	0.84[EUR][1000 genomes]
rs8036884	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037089	0.85[EUR][1000 genomes]
rs8038760	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs9806241	0.83[CHB][hapmap]
rs9920028	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9944207	1.00[CEU][hapmap];0.89[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
rs13380103	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs13380103	MAN2C1	cis	Stomach	GTEx
rs13380103	MAN2C1	cis	Thyroid	GTEx
rs13380103	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs13380103	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs13380103	MAN2C1	cis	lung	GTEx
rs13380103	MAN2C1	cis	Whole Blood	GTEx
rs13380103	MAN2C1	cis	Esophagus Mucosa	GTEx
rs13380103	MAN2C1	cis	Artery Aorta	GTEx
rs13380103	MAN2C1	cis	Artery Tibial	GTEx
rs13380103	MAN2C1	cis	Esophagus Muscularis	GTEx
rs13380103	MAN2C1	cis	Heart Left Ventricle	GTEx
rs13380103	MAN2C1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75872200-75876200	Weak transcription	Ovary	ovary
2	chr15:75872200-75888600	Weak transcription	Aorta	Aorta
3	chr15:75872400-75876000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:75872400-75876000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:75872400-75876000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:75872400-75876000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:75872400-75876200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:75872400-75876200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:75872400-75876200	Weak transcription	HSMM	muscle
10	chr15:75872400-75876200	Weak transcription	HSMMtube	muscle
11	chr15:75872400-75876200	Weak transcription	Osteobl	bone
12	chr15:75872400-75876400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:75872400-75876400	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:75872400-75876400	Weak transcription	HMEC	breast
15	chr15:75872400-75879800	Weak transcription	Fetal Stomach	stomach
16	chr15:75872400-75882600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:75872400-75882600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:75872400-75882600	Weak transcription	Adipose Nuclei	Adipose
19	chr15:75872400-75882600	Weak transcription	NHDF-Ad	bronchial
20	chr15:75872400-75882800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:75872400-75882800	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:75872400-75883000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:75872400-75883600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:75872400-75883600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:75872400-75883600	Weak transcription	Fetal Intestine Large	intestine
26	chr15:75872400-75883800	Weak transcription	Fetal Heart	heart
27	chr15:75872400-75884000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:75872400-75884000	Weak transcription	Spleen	Spleen
29	chr15:75872400-75884000	Weak transcription	NHEK	skin
30	chr15:75872400-75884200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:75872400-75884200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:75872400-75884200	Weak transcription	Left Ventricle	heart
33	chr15:75872400-75884200	Weak transcription	Stomach Mucosa	stomach
34	chr15:75872400-75884200	Weak transcription	GM12878-XiMat	blood
35	chr15:75872400-75885800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:75872400-75886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:75872400-75886000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:75872400-75886600	Weak transcription	Primary B cells from cord blood	blood
39	chr15:75872400-75886600	Weak transcription	Brain Anterior Caudate	brain
40	chr15:75872400-75886600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:75872400-75886600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:75872400-75886600	Weak transcription	NH-A	brain
43	chr15:75872400-75886800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:75872400-75886800	Weak transcription	Fetal Lung	lung
45	chr15:75872400-75887600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:75872400-75887800	Weak transcription	Brain Angular Gyrus	brain
47	chr15:75872400-75887800	Weak transcription	Lung	lung
48	chr15:75872400-75888000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr15:75872400-75888000	Weak transcription	Brain Substantia Nigra	brain
50	chr15:75872400-75888200	Weak transcription	NHLF	lung

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