Variant report

Variant	rs11547316
Chromosome Location	chr15:75909803-75909804
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	chr15:75907811..75910485-chr15:75930926..75933697,2	MCF-7	breast:
2	chr15:75908924..75911248-chr15:75931260..75932987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11632887	1.00[CHD][hapmap]
rs11634828	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11635996	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11638663	1.00[CHD][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	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
8	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
9	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11547316	MAN2C1	cis	Thyroid	GTEx
rs11547316	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs11547316	SNX33	cis	cerebellum	SCAN
rs11547316	MAN2C1	cis	parietal	SCAN
rs11547316	MAN2C1	cis	Whole Blood	GTEx
rs11547316	MAN2C1	cis	cerebellum	SCAN
rs11547316	MAN2C1	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75880400-75912400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:75882200-75910400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:75882800-75911400	Strong transcription	Fetal Muscle Leg	muscle
4	chr15:75883400-75911800	Strong transcription	Fetal Stomach	stomach
5	chr15:75883800-75911600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:75883800-75911800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr15:75886000-75912400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:75887600-75912400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:75889400-75917600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:75889800-75912600	Weak transcription	Right Atrium	heart
11	chr15:75889800-75917600	Weak transcription	Fetal Heart	heart
12	chr15:75890600-75917000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:75891000-75917200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:75891800-75912400	Weak transcription	Stomach Mucosa	stomach
15	chr15:75892000-75913200	Strong transcription	Liver	Liver
16	chr15:75894800-75910000	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr15:75894800-75913400	Strong transcription	Fetal Intestine Large	intestine
18	chr15:75896000-75911800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:75896000-75912400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:75896000-75913400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:75896200-75912000	Strong transcription	Placenta	Placenta
22	chr15:75896400-75913400	Strong transcription	Fetal Intestine Small	intestine
23	chr15:75896800-75913400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:75897000-75913000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:75897000-75914000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:75897400-75911800	Strong transcription	NHDF-Ad	bronchial
27	chr15:75897800-75913400	Strong transcription	Fetal Brain Female	brain
28	chr15:75898400-75911400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr15:75898600-75912400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr15:75899800-75912600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:75899800-75912600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:75900000-75912400	Strong transcription	Osteobl	bone
33	chr15:75900200-75911000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:75900600-75911800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:75901200-75911000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:75901200-75911600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:75901200-75912200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:75901200-75912600	Strong transcription	Primary T cells from cord blood	blood
39	chr15:75901200-75912600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:75901400-75912400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:75901400-75912600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:75901800-75912600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:75902000-75913000	Weak transcription	Small Intestine	intestine
44	chr15:75903000-75917600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr15:75904000-75913400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:75904200-75910200	Strong transcription	Brain Substantia Nigra	brain
47	chr15:75904200-75912400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:75904200-75912400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:75904400-75911200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:75904400-75912000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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