Variant report

Variant	rs4381565
Chromosome Location	chr15:75802154-75802155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75799580..75804058-chr15:75932687..75934537,4	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11634863	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11636031	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11636199	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11637068	0.81[AMR][1000 genomes]
rs11637586	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638974	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11639183	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12708518	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12708519	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708520	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12909863	0.84[EUR][1000 genomes]
rs12916964	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28432989	0.82[EUR][1000 genomes]
rs28610581	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28623700	0.80[EUR][1000 genomes]
rs28737338	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28783769	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4297648	0.81[AMR][1000 genomes]
rs4299117	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4322627	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4451914	0.81[AMR][1000 genomes]
rs4486847	0.81[AMR][1000 genomes]
rs4545784	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886443	0.85[AMR][1000 genomes]
rs4886446	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886703	0.81[AMR][1000 genomes]
rs4886707	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886708	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886712	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886715	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886716	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60972074	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62027181	0.82[EUR][1000 genomes]
rs6495182	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7163907	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171507	0.85[AMR][1000 genomes]
rs7176938	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7180574	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7184046	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7495610	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8023268	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023815	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024244	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027365	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027546	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029112	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030802	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034317	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8036758	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038760	0.84[AMR][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	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4381565	MAN2C1	cis	Nerve Tibial	GTEx
rs4381565	MAN2C1	cis	Heart Left Ventricle	GTEx
rs4381565	MAN2C1	cis	Esophagus Mucosa	GTEx
rs4381565	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs4381565	MAN2C1	cis	Stomach	GTEx
rs4381565	MAN2C1	cis	lung	GTEx
rs4381565	MAN2C1	cis	Artery Tibial	GTEx
rs4381565	MAN2C1	cis	Whole Blood	GTEx
rs4381565	MAN2C1	cis	Thyroid	GTEx
rs4381565	MAN2C1	cis	Esophagus Muscularis	GTEx
rs4381565	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs4381565	MAN2C1	cis	Artery Aorta	GTEx
rs4381565	SNUPN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75777200-75816800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75777600-75812000	Weak transcription	Small Intestine	intestine
3	chr15:75780200-75812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:75782600-75815200	Weak transcription	K562	blood
5	chr15:75785600-75814200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:75790000-75814200	Weak transcription	Psoas Muscle	Psoas
7	chr15:75797800-75803200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:75797800-75806200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:75797800-75819600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:75797800-75819600	Strong transcription	Fetal Stomach	stomach
11	chr15:75797800-75820000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:75798400-75805400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75798400-75824800	Weak transcription	Stomach Mucosa	stomach
14	chr15:75798400-75825000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:75798600-75807600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:75798600-75818800	Weak transcription	Fetal Heart	heart
17	chr15:75798800-75820400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75799000-75804600	Weak transcription	Brain Substantia Nigra	brain
19	chr15:75799000-75813200	Weak transcription	Aorta	Aorta
20	chr15:75799200-75805200	Weak transcription	HepG2	liver
21	chr15:75799200-75812800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:75799200-75814000	Weak transcription	Fetal Brain Male	brain
23	chr15:75799200-75814800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:75799400-75803600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:75799400-75804800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:75799400-75805200	Weak transcription	Brain Angular Gyrus	brain
27	chr15:75799400-75805200	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:75799400-75805200	Weak transcription	Ovary	ovary
29	chr15:75799400-75805200	Weak transcription	Thymus	Thymus
30	chr15:75799400-75805600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:75799400-75805800	Weak transcription	Gastric	stomach
32	chr15:75799400-75807600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:75799400-75808800	Weak transcription	Fetal Kidney	kidney
34	chr15:75799400-75809400	Weak transcription	Primary B cells from cord blood	blood
35	chr15:75799400-75809600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:75799400-75809600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:75799400-75812200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:75799400-75814200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:75799400-75814200	Weak transcription	Pancreas	Pancrea
40	chr15:75799400-75818000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:75799400-75819400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:75799400-75821800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:75799600-75803600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:75799600-75804600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:75799600-75805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:75799600-75805400	Weak transcription	Colonic Mucosa	Colon
47	chr15:75799600-75807600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:75799600-75813200	Weak transcription	Esophagus	oesophagus
49	chr15:75799800-75804600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:75799800-75804600	Weak transcription	Spleen	Spleen

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