Variant report

Variant	rs7173220
Chromosome Location	chr15:75712933-75712934
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11072544	0.92[EUR][1000 genomes]
rs1128933	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632813	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637263	0.86[EUR][1000 genomes]
rs12324230	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903362	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909709	0.82[AFR][1000 genomes]
rs12911512	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809549	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4526985	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886442	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886702	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886704	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886705	0.88[EUR][1000 genomes]
rs4886706	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495173	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495174	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495176	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495178	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495181	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7163783	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164541	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7165292	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165469	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7170660	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175139	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182283	0.90[EUR][1000 genomes]
rs73436868	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8030014	0.89[EUR][1000 genomes]
rs9806241	0.86[EUR][1000 genomes];0.89[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7173220	MAN2C1	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75662200-75715600	Strong transcription	Placenta	Placenta
2	chr15:75662400-75717000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:75662400-75731400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:75662600-75722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:75662800-75723000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:75663400-75713000	Strong transcription	Thymus	Thymus
7	chr15:75665800-75723200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:75671400-75717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:75683000-75730200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:75684400-75717800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:75690400-75715600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:75703200-75715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75703200-75732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:75704200-75714400	Weak transcription	Small Intestine	intestine
15	chr15:75704200-75714800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:75704800-75713200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:75704800-75728200	Weak transcription	Psoas Muscle	Psoas
18	chr15:75704800-75742200	Weak transcription	Fetal Brain Male	brain
19	chr15:75705200-75713000	Weak transcription	NH-A	brain
20	chr15:75705200-75714200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:75705200-75738200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:75705400-75713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:75705400-75713200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:75705400-75713200	Weak transcription	Brain Germinal Matrix	brain
25	chr15:75705400-75713800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:75705400-75714000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:75705400-75714200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:75705400-75714200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:75705400-75714200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:75705400-75714200	Weak transcription	HSMMtube	muscle
31	chr15:75705400-75714400	Weak transcription	Colonic Mucosa	Colon
32	chr15:75705400-75714400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:75705400-75714400	Weak transcription	Spleen	Spleen
34	chr15:75705400-75714800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:75705400-75714800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:75705400-75714800	Weak transcription	Pancreas	Pancrea
37	chr15:75705400-75714800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:75705400-75718400	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:75705400-75720600	Weak transcription	Aorta	Aorta
40	chr15:75705400-75722600	Weak transcription	Gastric	stomach
41	chr15:75705400-75724600	Weak transcription	Fetal Heart	heart
42	chr15:75705400-75741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:75705400-75742200	Weak transcription	Right Ventricle	heart
44	chr15:75705600-75714400	Weak transcription	Left Ventricle	heart
45	chr15:75705600-75715000	Weak transcription	Esophagus	oesophagus
46	chr15:75705600-75720400	Weak transcription	Brain Angular Gyrus	brain
47	chr15:75705800-75714200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:75705800-75714400	Weak transcription	Lung	lung
49	chr15:75706000-75719000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:75706400-75713800	Weak transcription	Ovary	ovary

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