Variant report

Variant	rs4886452
Chromosome Location	chr15:75929756-75929757
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75868548..75873773-chr15:75928671..75933652,6	K562	blood:
2	chr15:75868548..75873380-chr15:75928279..75933652,7	K562	blood:
3	chr15:75742140..75749687-chr15:75929409..75934974,27	MCF-7	breast:
4	chr15:75741578..75748579-chr15:75928515..75935579,16	K562	blood:
5	chr15:75657323..75661859-chr15:75928778..75934895,5	K562	blood:
6	chr15:75869532..75872781-chr15:75929534..75934767,14	MCF-7	breast:
7	chr15:75657489..75661684-chr15:75927450..75931877,5	K562	blood:
8	chr15:75929384..75930016-chr17:62502373..62503322,2	HCT-116	colon:
9	chr15:75929555..75932491-chr15:75973247..75974868,2	MCF-7	breast:
10	chr15:75741578..75748624-chr15:75927989..75935113,20	K562	blood:
11	chr15:75916634..75921269-chr15:75928640..75933625,8	MCF-7	breast:
12	chr15:75898763..75900517-chr15:75928624..75930263,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108654	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000169371	Chromatin interaction
ENSG00000169410	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000260235	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000258890	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10163126	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10851882	0.88[CEU][hapmap]
rs11072552	0.92[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs11632105	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs11632813	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11634402	0.92[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11855087	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs12101874	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12324230	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs12911229	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28376842	0.82[ASN][1000 genomes]
rs4430707	0.88[CEU][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap]
rs4886450	0.84[EUR][1000 genomes]
rs4886704	0.88[CEU][hapmap]
rs4886705	0.88[CEU][hapmap]
rs4886706	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4886718	0.92[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6495176	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6495181	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7164541	0.88[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs8023495	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8026113	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8042772	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9806241	0.88[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4886452	MAN2C1	cis	multi-tissue	Pritchard
rs4886452	MAN2C1	cis	Nerve Tibial	GTEx
rs4886452	PSTPIP1	cis	parietal	SCAN
rs4886452	SNUPN	cis	parietal	SCAN
rs4886452	DDX51	trans	parietal	SCAN
rs4886452	RCN2	cis	cerebellum	SCAN
rs4886452	MAN2C1	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75918600-75931000	Weak transcription	Aorta	Aorta
2	chr15:75918800-75929800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr15:75918800-75930200	Weak transcription	HUVEC	blood vessel
4	chr15:75918800-75930400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75918800-75930600	Weak transcription	Right Atrium	heart
6	chr15:75919000-75929800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:75919000-75929800	Weak transcription	Osteobl	bone
8	chr15:75919200-75930200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:75920600-75930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:75926400-75930000	Weak transcription	Brain Substantia Nigra	brain
11	chr15:75927000-75929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:75927200-75929800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:75927600-75930000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:75927600-75930800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:75928200-75929800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:75928400-75929800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:75928600-75929800	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:75928600-75929800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:75928600-75930400	Genic enhancers	Fetal Intestine Small	intestine
20	chr15:75928600-75930600	Enhancers	Liver	Liver
21	chr15:75929200-75930000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:75929200-75930000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:75929200-75930200	Enhancers	Adipose Nuclei	Adipose
24	chr15:75929200-75930400	Genic enhancers	Brain Germinal Matrix	brain
25	chr15:75929200-75931000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr15:75929400-75929800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr15:75929400-75929800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:75929400-75929800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:75929400-75929800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:75929400-75929800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:75929400-75929800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:75929400-75929800	Genic enhancers	Thymus	Thymus
33	chr15:75929400-75929800	Enhancers	HepG2	liver
34	chr15:75929400-75930000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:75929400-75930000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:75929400-75930000	Genic enhancers	Primary hematopoietic stem cells	blood
37	chr15:75929400-75930000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr15:75929400-75930200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr15:75929400-75930200	Genic enhancers	Fetal Stomach	stomach
40	chr15:75929400-75930400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:75929400-75930400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr15:75929400-75930400	Enhancers	Colonic Mucosa	Colon
43	chr15:75929400-75930400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:75929400-75930400	Genic enhancers	Fetal Muscle Leg	muscle
45	chr15:75929400-75930400	Enhancers	Lung	lung
46	chr15:75929400-75930400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr15:75929400-75930600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:75929400-75930600	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr15:75929400-75930600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:75929400-75930800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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