Variant report

Variant	rs28737338
Chromosome Location	chr15:75768679-75768680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75767969..75769622-chr15:75930822..75933401,2	MCF-7	breast:
2	chr15:75745748..75747907-chr15:75768138..75770692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10152155	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10220738	0.83[EUR][1000 genomes]
rs10775209	0.82[EUR][1000 genomes]
rs10851882	0.80[ASN][1000 genomes]
rs11072542	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11072544	0.81[ASN][1000 genomes]
rs11631052	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11634863	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11636031	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11636199	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637068	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637263	0.92[ASN][1000 genomes]
rs11637586	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11638974	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639183	0.88[EUR][1000 genomes]
rs12708518	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12708519	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12708520	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12909863	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916964	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13380103	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28432989	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28610581	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28623700	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28693593	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28783769	0.83[EUR][1000 genomes]
rs3809547	0.80[EUR][1000 genomes]
rs4075522	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4243033	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4297648	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299117	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4322627	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4368141	0.84[EUR][1000 genomes]
rs4381565	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4451914	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4462560	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4486847	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4545784	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4564532	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886443	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886699	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886700	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886703	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886704	0.85[ASN][1000 genomes]
rs4886705	0.84[ASN][1000 genomes]
rs4886707	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886712	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886715	0.85[EUR][1000 genomes]
rs4886716	0.83[EUR][1000 genomes]
rs5745920	0.82[EUR][1000 genomes]
rs60972074	0.83[EUR][1000 genomes]
rs62027181	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495174	0.85[ASN][1000 genomes]
rs6495182	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7163451	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7163907	0.85[EUR][1000 genomes]
rs7165469	0.83[ASN][1000 genomes]
rs7166737	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170660	0.85[ASN][1000 genomes]
rs7171507	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7175852	0.85[EUR][1000 genomes]
rs7176938	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7180574	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7184046	0.82[EUR][1000 genomes]
rs7402293	0.82[EUR][1000 genomes]
rs7402844	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7495610	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8023268	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8023815	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8024244	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8027365	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8027546	0.89[EUR][1000 genomes]
rs8028277	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8029112	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8029394	0.84[EUR][1000 genomes]
rs8030802	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8034317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8035987	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8036758	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8036884	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8038760	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv904387	chr15:75706296-75806911	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	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
10	nsv904388	chr15:75730182-75804543	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	nsv904389	chr15:75739824-75806911	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv827390	chr15:75766087-75795370	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs28737338	MAN2C1	cis	Thyroid	GTEx
rs28737338	MAN2C1	cis	lung	GTEx
rs28737338	SNUPN	cis	Thyroid	GTEx
rs28737338	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs28737338	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs28737338	MAN2C1	cis	Stomach	GTEx
rs28737338	MAN2C1	cis	Whole Blood	GTEx
rs28737338	MAN2C1	cis	Artery Tibial	GTEx
rs28737338	MAN2C1	cis	Nerve Tibial	GTEx
rs28737338	MAN2C1	cis	Esophagus Muscularis	GTEx
rs28737338	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs28737338	MAN2C1	cis	Heart Left Ventricle	GTEx
rs28737338	MAN2C1	cis	Artery Aorta	GTEx
rs28737338	MAN2C1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75749000-75797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:75749200-75776800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:75749200-75782000	Weak transcription	Right Atrium	heart
4	chr15:75754400-75770800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:75755200-75772400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:75755200-75772400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:75755200-75772600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:75755400-75772400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:75755600-75769800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:75755600-75772800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:75756200-75772400	Strong transcription	Fetal Stomach	stomach
12	chr15:75756200-75772600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:75756200-75772600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:75756400-75772600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr15:75756600-75772800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:75756800-75769800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr15:75757200-75770400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr15:75757400-75772400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:75757600-75769600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:75757800-75769800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:75757800-75769800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:75757800-75769800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:75757800-75772600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:75758000-75769400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr15:75758000-75769400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:75758000-75772400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:75758000-75772400	Strong transcription	Liver	Liver
28	chr15:75758000-75772400	Strong transcription	Osteobl	bone
29	chr15:75758000-75772600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:75758000-75772800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:75758200-75769600	Strong transcription	Fetal Thymus	thymus
32	chr15:75758200-75769800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:75758200-75770000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:75758200-75772200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr15:75758400-75769400	Strong transcription	Placenta	Placenta
36	chr15:75758400-75769600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:75758400-75769800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:75758400-75772200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:75758600-75769600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:75758600-75772000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:75758600-75772200	Strong transcription	Fetal Intestine Small	intestine
42	chr15:75758800-75769600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:75761600-75785200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr15:75761800-75772600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr15:75762000-75771600	Weak transcription	Stomach Mucosa	stomach
46	chr15:75762200-75769800	Strong transcription	Left Ventricle	heart
47	chr15:75762200-75775400	Weak transcription	Fetal Heart	heart
48	chr15:75762200-75798000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:75762400-75771800	Weak transcription	Right Ventricle	heart
50	chr15:75762400-75771800	Weak transcription	K562	blood

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