Variant report

Variant	rs7166436
Chromosome Location	chr15:75630635-75630636
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75630574-75630778	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:75630524-75630835	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:75630516-75630691	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:75630524-75630793	HepG2	liver:	n/a	n/a
5	POLR2A	chr15:75630590-75630706	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:75630269-75630889	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:75630489-75630976	H1-hESC	embryonic stem cell:	n/a	n/a
8	HEY1	chr15:75630410-75630826	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:75630500-75630777	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75630334..75631987-chr15:75656015..75658534,2	MCF-7	breast:
2	chr15:75628015..75635137-chr15:75659177..75662618,8	MCF-7	breast:
3	chr15:75628778..75631510-chr15:75648708..75650958,2	MCF-7	breast:
4	chr15:75630305..75632330-chr15:75638172..75640070,3	MCF-7	breast:

No data

Variant related genes	Relation type
COMMD4	TF binding region
ENSG00000260274	Chromatin interaction
ENSG00000140398	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11634109	0.90[EUR][1000 genomes]
rs1809714	0.90[EUR][1000 genomes]
rs1984586	0.90[EUR][1000 genomes]
rs1984587	0.88[EUR][1000 genomes]
rs3866545	0.90[EUR][1000 genomes]
rs4310817	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886684	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55653892	0.90[EUR][1000 genomes]
rs56164452	0.92[EUR][1000 genomes]
rs59084522	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164167	0.91[EUR][1000 genomes]
rs7164429	0.91[EUR][1000 genomes]
rs7166852	0.89[EUR][1000 genomes]
rs7167401	0.90[EUR][1000 genomes]
rs7183520	0.90[EUR][1000 genomes]
rs73435015	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73435089	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73436803	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8031650	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9673084	0.88[EUR][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	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription 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	94 gene(s)	inside rSNPs	diseases
4	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv977736	chr15:75509295-75632679	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7166436	MAN2C1	cis	Esophagus Muscularis	GTEx
rs7166436	SNUPN	cis	Thyroid	GTEx
rs7166436	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75629200-75631000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:75629200-75631000	Weak transcription	Esophagus	oesophagus
3	chr15:75629200-75631200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:75629200-75631200	Weak transcription	Brain Anterior Caudate	brain
5	chr15:75629200-75631600	Weak transcription	Ovary	ovary
6	chr15:75629200-75636200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:75629200-75638800	Weak transcription	Primary B cells from cord blood	blood
8	chr15:75629200-75639000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:75629200-75639000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:75629200-75639000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:75629200-75639200	Weak transcription	Aorta	Aorta
12	chr15:75629200-75639200	Weak transcription	Small Intestine	intestine
13	chr15:75629400-75630800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:75629400-75630800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:75629400-75630800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:75629400-75630800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:75629400-75630800	Weak transcription	Fetal Intestine Small	intestine
18	chr15:75629400-75630800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:75629400-75631000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:75629400-75631000	Weak transcription	Placenta	Placenta
21	chr15:75629400-75631000	Weak transcription	Gastric	stomach
22	chr15:75629400-75631000	Weak transcription	Pancreas	Pancrea
23	chr15:75629400-75631000	Weak transcription	Spleen	Spleen
24	chr15:75629400-75631000	Weak transcription	NHLF	lung
25	chr15:75629400-75631200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:75629400-75631200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:75629400-75631200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:75629400-75631200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:75629400-75631200	Weak transcription	Osteobl	bone
30	chr15:75629400-75631600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:75629400-75631600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:75629400-75631600	Weak transcription	HSMMtube	muscle
33	chr15:75629400-75631800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:75629400-75631800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:75629400-75631800	Weak transcription	Brain Substantia Nigra	brain
36	chr15:75629400-75631800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:75629400-75631800	Weak transcription	HMEC	breast
38	chr15:75629400-75632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:75629400-75632000	Weak transcription	Primary T cells from cord blood	blood
40	chr15:75629400-75632000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:75629400-75632200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr15:75629400-75632400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr15:75629400-75634800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:75629400-75635000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:75629400-75636200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:75629400-75637600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr15:75629400-75638400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:75629400-75638800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:75629400-75639000	Weak transcription	Brain Angular Gyrus	brain
50	chr15:75629400-75639000	Weak transcription	Colonic Mucosa	Colon

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