Variant report

Variant	rs4886722
Chromosome Location	chr15:75921636-75921637
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75916258..75921824-chr15:75930808..75933710,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10163126	0.91[ASN][1000 genomes]
rs10851882	0.87[GIH][hapmap]
rs11072552	0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11072553	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632105	0.84[GIH][hapmap]
rs11632813	0.85[GIH][hapmap]
rs11634402	0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11636031	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11636199	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs11638974	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs11856606	0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12101874	0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12324230	0.85[GIH][hapmap]
rs12708519	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12708520	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12909863	0.84[EUR][1000 genomes]
rs12910672	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911229	0.92[ASN][1000 genomes]
rs13380103	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13737	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28610581	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs28623700	0.84[EUR][1000 genomes]
rs28693593	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs28783769	0.98[GIH][hapmap];0.84[EUR][1000 genomes]
rs4075522	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4299117	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs4322627	0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4371118	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4430707	0.87[GIH][hapmap]
rs4451914	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs4545784	1.00[CEU][hapmap]
rs4886443	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs4886446	1.00[CEU][hapmap];0.95[GIH][hapmap]
rs4886450	0.91[ASN][1000 genomes]
rs4886702	0.85[GIH][hapmap]
rs4886703	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs4886704	0.85[GIH][hapmap]
rs4886707	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs4886708	0.94[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs4886715	0.84[EUR][1000 genomes]
rs4886716	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4886718	0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4886719	0.90[ASN][1000 genomes]
rs4886720	0.91[ASN][1000 genomes]
rs60972074	0.84[EUR][1000 genomes]
rs62027181	0.84[EUR][1000 genomes]
rs62027209	0.81[EUR][1000 genomes]
rs6495176	0.85[GIH][hapmap]
rs6495181	0.85[GIH][hapmap]
rs6495182	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7163451	0.84[EUR][1000 genomes]
rs7163907	1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs7164541	0.87[GIH][hapmap]
rs7166281	0.88[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170787	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7175223	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180574	0.80[EUR][1000 genomes]
rs7184046	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs8023268	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8023495	0.87[ASN][1000 genomes]
rs8023815	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs8024244	0.80[EUR][1000 genomes]
rs8026113	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8029112	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs8030802	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs8034317	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs8036758	0.80[EUR][1000 genomes]
rs8036884	0.86[EUR][1000 genomes]
rs8037089	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038760	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs8042772	0.93[ASN][1000 genomes]
rs9806241	0.85[GIH][hapmap]
rs9920028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9920034	0.86[EUR][1000 genomes]
rs9944207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4886722	MAN2C1	cis	Esophagus Muscularis	GTEx
rs4886722	MAN2C1	cis	lung	GTEx
rs4886722	MAN2C1	cis	Artery Tibial	GTEx
rs4886722	MAN2C1	cis	parietal	SCAN
rs4886722	MAN2C1	cis	Esophagus Mucosa	GTEx
rs4886722	SNUPN	cis	lymphoblastoid	seeQTL
rs4886722	MAN2C1	cis	Heart Left Ventricle	GTEx
rs4886722	MAN2C1	cis	Nerve Tibial	GTEx
rs4886722	MAN2C1	cis	Artery Aorta	GTEx
rs4886722	MAN2C1	cis	Thyroid	GTEx
rs4886722	MAN2C1	cis	Stomach	GTEx
rs4886722	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs4886722	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs4886722	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs4886722	MAN2C1	cis	Whole Blood	GTEx
rs4886722	MAN2C1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75918600-75931000	Weak transcription	Aorta	Aorta
2	chr15:75918800-75926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:75918800-75929200	Weak transcription	Brain Germinal Matrix	brain
4	chr15:75918800-75929400	Weak transcription	Psoas Muscle	Psoas
5	chr15:75918800-75929600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:75918800-75929600	Weak transcription	Brain Angular Gyrus	brain
7	chr15:75918800-75929600	Weak transcription	Brain Anterior Caudate	brain
8	chr15:75918800-75929600	Weak transcription	Spleen	Spleen
9	chr15:75918800-75929600	Weak transcription	HSMM	muscle
10	chr15:75918800-75929800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:75918800-75930200	Weak transcription	HUVEC	blood vessel
12	chr15:75918800-75930400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75918800-75930600	Weak transcription	Right Atrium	heart
14	chr15:75919000-75929200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:75919000-75929400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:75919000-75929400	Weak transcription	Fetal Stomach	stomach
17	chr15:75919000-75929400	Weak transcription	Thymus	Thymus
18	chr15:75919000-75929600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:75919000-75929600	Weak transcription	Fetal Brain Female	brain
20	chr15:75919000-75929600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:75919000-75929800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:75919000-75929800	Weak transcription	Osteobl	bone
23	chr15:75919200-75926800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:75919200-75928000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:75919200-75928200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:75919200-75928200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:75919200-75928600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:75919200-75929400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:75919200-75929400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:75919200-75929600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:75919200-75929600	Weak transcription	Primary B cells from cord blood	blood
32	chr15:75919200-75929600	Weak transcription	Primary T cells from cord blood	blood
33	chr15:75919200-75929600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:75919200-75929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:75919200-75929600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:75919200-75929600	Weak transcription	Fetal Lung	lung
37	chr15:75919200-75930200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:75919800-75929200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:75919800-75929600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr15:75920000-75926800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:75920200-75929200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:75920200-75929400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:75920400-75924400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:75920400-75926800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:75920400-75927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:75920400-75927600	Weak transcription	A549	lung
47	chr15:75920400-75928400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:75920600-75924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:75920600-75924400	Weak transcription	HMEC	breast
50	chr15:75920600-75930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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