Variant report

Variant	rs7175139
Chromosome Location	chr15:75734317-75734318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75733027..75735420-chr15:75931061..75932964,2	MCF-7	breast:
2	chr15:75660231..75661838-chr15:75732480..75735371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072544	0.92[EUR][1000 genomes]
rs1128933	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632813	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637263	0.88[EUR][1000 genomes]
rs12324230	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12903362	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909709	0.81[EUR][1000 genomes]
rs12911512	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915221	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809549	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4526985	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886442	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886702	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886704	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886705	0.90[EUR][1000 genomes]
rs4886706	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495172	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6495173	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495174	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495176	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495178	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495181	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7163783	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164541	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165292	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165469	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7170660	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7173220	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182283	0.89[EUR][1000 genomes]
rs73436868	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030014	0.86[EUR][1000 genomes]
rs8043300	0.81[EUR][1000 genomes]
rs9806241	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7175139	MAN2C1	cis	Whole Blood	GTEx
rs7175139	MAN2C1	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75704800-75742200	Weak transcription	Fetal Brain Male	brain
2	chr15:75705200-75738200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:75705400-75741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75705400-75742200	Weak transcription	Right Ventricle	heart
5	chr15:75708800-75740400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:75715200-75735400	Weak transcription	Colonic Mucosa	Colon
7	chr15:75715400-75741400	Weak transcription	Small Intestine	intestine
8	chr15:75715600-75742200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:75716200-75738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:75717000-75742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:75721200-75739600	Weak transcription	Brain Substantia Nigra	brain
12	chr15:75721200-75742600	Weak transcription	Aorta	Aorta
13	chr15:75721800-75735400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:75721800-75739600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:75721800-75742000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:75722000-75741600	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:75722200-75738200	Weak transcription	Fetal Kidney	kidney
18	chr15:75722200-75742000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:75722400-75735800	Weak transcription	NHDF-Ad	bronchial
20	chr15:75722600-75741600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:75722600-75742000	Weak transcription	Brain Anterior Caudate	brain
22	chr15:75722800-75734600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:75722800-75734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:75722800-75734800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:75722800-75735400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:75722800-75735600	Weak transcription	Fetal Lung	lung
27	chr15:75722800-75735600	Weak transcription	NHLF	lung
28	chr15:75722800-75735800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:75722800-75735800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:75722800-75738200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:75722800-75738600	Weak transcription	Spleen	Spleen
32	chr15:75722800-75741000	Weak transcription	Brain Germinal Matrix	brain
33	chr15:75722800-75741400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:75722800-75741600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:75722800-75741600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:75722800-75742000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:75722800-75742200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:75722800-75742200	Weak transcription	Gastric	stomach
39	chr15:75722800-75742200	Weak transcription	Pancreas	Pancrea
40	chr15:75722800-75742200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:75722800-75742200	Weak transcription	HSMMtube	muscle
42	chr15:75723000-75735400	Weak transcription	Placenta	Placenta
43	chr15:75723000-75740200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:75723000-75742600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:75723800-75736200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:75724400-75735400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:75724600-75735200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:75724600-75736000	Weak transcription	NH-A	brain
49	chr15:75724600-75736200	Weak transcription	HSMM	muscle
50	chr15:75727800-75735200	Weak transcription	K562	blood

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