Variant report

Variant	rs12909863
Chromosome Location	chr15:75825822-75825823
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75823394..75827667-chr15:75930118..75933171,4	MCF-7	breast:
2	chr15:75824690..75826344-chr15:75835953..75838472,2	K562	blood:
3	chr15:75745002..75747584-chr15:75825328..75827934,2	K562	blood:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10851882	0.89[ASN][1000 genomes]
rs11634863	0.86[EUR][1000 genomes]
rs11635080	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636031	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11636199	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637586	0.89[EUR][1000 genomes]
rs11638974	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639183	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12708518	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12708519	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12708520	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910672	0.83[EUR][1000 genomes]
rs12916256	0.86[ASN][1000 genomes]
rs12916964	0.89[EUR][1000 genomes]
rs13380103	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28432989	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28610581	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28623700	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28693593	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28737338	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28783769	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4075522	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4299117	0.89[EUR][1000 genomes]
rs4322627	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4381565	0.84[EUR][1000 genomes]
rs4393535	0.87[EUR][1000 genomes]
rs4545784	0.83[EUR][1000 genomes]
rs4564532	0.80[EUR][1000 genomes]
rs4886446	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886699	0.80[EUR][1000 genomes]
rs4886707	0.83[EUR][1000 genomes]
rs4886708	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886712	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886715	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4886716	0.94[EUR][1000 genomes]
rs4886722	0.84[EUR][1000 genomes]
rs60972074	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62027181	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62027209	0.88[EUR][1000 genomes]
rs6495182	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7163451	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7163907	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7170787	0.86[EUR][1000 genomes]
rs7175223	0.81[EUR][1000 genomes]
rs7176938	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7176989	0.91[ASN][1000 genomes]
rs7180574	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7184046	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7495610	0.89[EUR][1000 genomes]
rs8023268	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8023815	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8024244	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8027365	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8027546	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8029112	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8030802	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8034317	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036758	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8036884	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037089	0.83[EUR][1000 genomes]
rs9920028	0.84[EUR][1000 genomes]
rs9944207	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv904390	chr15:75795177-75840943	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv819520	chr15:75819453-75865881	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12909863	MAN2C1	cis	lung	GTEx
rs12909863	MAN2C1	cis	Artery Tibial	GTEx
rs12909863	MAN2C1	cis	Esophagus Muscularis	GTEx
rs12909863	MAN2C1	cis	Whole Blood	GTEx
rs12909863	MAN2C1	cis	Heart Left Ventricle	GTEx
rs12909863	MAN2C1	cis	Esophagus Mucosa	GTEx
rs12909863	MAN2C1	cis	Stomach	GTEx
rs12909863	MAN2C1	cis	Artery Aorta	GTEx
rs12909863	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs12909863	MAN2C1	cis	Thyroid	GTEx
rs12909863	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs12909863	MAN2C1	cis	Nerve Tibial	GTEx
rs12909863	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs12909863	SNUPN	cis	Whole Blood	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75803200-75828000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:75814600-75826400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:75816000-75838000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:75817800-75843200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:75819600-75832400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:75819600-75834200	Weak transcription	Fetal Intestine Large	intestine
7	chr15:75819600-75834600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:75819600-75834600	Weak transcription	GM12878-XiMat	blood
9	chr15:75819600-75834800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:75819600-75836600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:75819600-75836600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:75819600-75837400	Weak transcription	Spleen	Spleen
13	chr15:75819600-75865000	Weak transcription	Primary B cells from cord blood	blood
14	chr15:75819600-75866200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:75819600-75869200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:75819800-75832000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:75819800-75834600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:75819800-75834800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr15:75819800-75836600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:75819800-75836600	Weak transcription	Dnd41	blood
21	chr15:75819800-75839000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:75819800-75840200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:75819800-75860800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr15:75819800-75869600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:75820000-75835600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:75820000-75835600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr15:75820000-75844000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:75820400-75836200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:75823400-75826000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:75823400-75826000	Enhancers	Fetal Muscle Leg	muscle
31	chr15:75823400-75826000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:75823400-75826200	Enhancers	HSMM	muscle
33	chr15:75823400-75826200	Enhancers	NHDF-Ad	bronchial
34	chr15:75823400-75826400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:75823400-75826400	Enhancers	HMEC	breast
36	chr15:75823400-75826600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:75823400-75827000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:75823600-75826000	Enhancers	Ovary	ovary
39	chr15:75823600-75832800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:75823800-75826000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:75823800-75826200	Enhancers	Stomach Smooth Muscle	stomach
42	chr15:75823800-75826400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:75823800-75837400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:75823800-75839000	Weak transcription	Fetal Brain Female	brain
45	chr15:75823800-75858000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:75823800-75869600	Weak transcription	Fetal Thymus	thymus
47	chr15:75824000-75826000	Enhancers	Adipose Nuclei	Adipose
48	chr15:75824400-75826000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:75824400-75826400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr15:75824400-75826600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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