Variant report

Variant	rs7178506
Chromosome Location	chr15:41096097-41096098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:41095980-41096130	HCT-116	colon:	n/a	chr15:41096103-41096112
2	CTCF	chr15:41095980-41096130	HBMEC	blood vessel:	n/a	chr15:41096103-41096112
3	CTCF	chr15:41096040-41096190	Hela-S3	cervix:	n/a	chr15:41096103-41096112
4	CTCF	chr15:41096060-41096210	GM12869	blood:	n/a	chr15:41096103-41096112
5	CTCF	chr15:41096020-41096170	GM12865	blood:	n/a	chr15:41096103-41096112
6	CTCF	chr15:41096000-41096150	HBMEC	blood vessel:	n/a	chr15:41096103-41096112
7	CTCF	chr15:41096060-41096210	GM12867	blood:	n/a	chr15:41096103-41096112
8	CTCF	chr15:41096020-41096170	GM12873	blood:	n/a	chr15:41096103-41096112
9	CTCF	chr15:41096060-41096210	GM12878	blood:	n/a	chr15:41096103-41096112
10	CTCF	chr15:41096020-41096170	HEK293	kidney:	n/a	chr15:41096103-41096112
11	RAD21	chr15:41095950-41096211	HepG2	liver:	n/a	chr15:41096048-41096061
12	CTCF	chr15:41096000-41096150	HepG2	liver:	n/a	chr15:41096103-41096112
13	CTCF	chr15:41096047-41096135	K562	blood:	n/a	chr15:41096103-41096112
14	CTCF	chr15:41096040-41096190	GM12872	blood:	n/a	chr15:41096103-41096112
15	CTCF	chr15:41096061-41096135	MCF-7	breast:	n/a	chr15:41096103-41096112
16	CTCF	chr15:41096060-41096210	GM12864	blood:	n/a	chr15:41096103-41096112
17	CTCF	chr15:41096000-41096150	Caco-2	colon:	n/a	chr15:41096103-41096112
18	CTCF	chr15:41096000-41096150	HPF	lung:	n/a	chr15:41096103-41096112
19	CTCF	chr15:41096040-41096190	RPTEC	kidney:	n/a	chr15:41096103-41096112
20	CTCF	chr15:41096080-41096230	AoAF	blood vessel:	n/a	chr15:41096103-41096112
21	CTCF	chr15:41096000-41096150	NB4	blood:	n/a	chr15:41096103-41096112
22	CTCF	chr15:41096005-41096181	HepG2	liver:	n/a	chr15:41096103-41096112
23	CTCF	chr15:41096060-41096210	GM12873	blood:	n/a	chr15:41096103-41096112
24	CTCF	chr15:41095980-41096130	SK-N-SH_RA	brain:	n/a	chr15:41096103-41096112
25	RAD21	chr15:41095985-41096137	HepG2	liver:	n/a	chr15:41096048-41096061
26	CTCF	chr15:41095960-41096110	GM12874	blood:	n/a	n/a
27	CTCF	chr15:41095960-41096110	NHEK	skin:	n/a	n/a
28	CTCF	chr15:41096020-41096170	GM12875	blood:	n/a	chr15:41096103-41096112
29	CTCF	chr15:41096046-41096130	K562	blood:	n/a	chr15:41096103-41096112
30	CTCF	chr15:41096040-41096190	GM12866	blood:	n/a	chr15:41096103-41096112
31	CTCF	chr15:41096060-41096210	SK-N-SH_RA	brain:	n/a	chr15:41096103-41096112
32	CTCF	chr15:41096020-41096170	HepG2	liver:	n/a	chr15:41096103-41096112
33	CTCF	chr15:41096060-41096210	WERI-Rb-1	eye:	n/a	chr15:41096103-41096112
34	CTCF	chr15:41096000-41096150	GM12874	blood:	n/a	chr15:41096103-41096112
35	CTCF	chr15:41095980-41096130	Hela-S3	cervix:	n/a	chr15:41096103-41096112
36	CTCF	chr15:41096091-41096150	HepG2	liver:	n/a	chr15:41096103-41096112
37	CTCF	chr15:41096052-41096135	GM12891	blood:	n/a	chr15:41096103-41096112
38	RAD21	chr15:41095984-41096221	HepG2	liver:	n/a	chr15:41096048-41096061
39	CTCF	chr15:41096060-41096210	GM12871	blood:	n/a	chr15:41096103-41096112
40	CTCF	chr15:41096020-41096170	GM12878	blood:	n/a	chr15:41096103-41096112
41	SMC3	chr15:41095973-41096189	HepG2	liver:	n/a	n/a
42	CTCF	chr15:41096056-41096133	Hela-S3	cervix:	n/a	chr15:41096103-41096112
43	CTCF	chr15:41096047-41096115	MCF-7	breast:	n/a	chr15:41096103-41096112
44	CTCF	chr15:41096040-41096190	GM06990	blood:	n/a	chr15:41096103-41096112
45	CTCF	chr15:41095980-41096130	RPTEC	kidney:	n/a	chr15:41096103-41096112
46	CTCF	chr15:41096000-41096150	GM12865	blood:	n/a	chr15:41096103-41096112
47	CTCF	chr15:41096020-41096170	GM12871	blood:	n/a	chr15:41096103-41096112
48	CTCF	chr15:41096060-41096210	GM12866	blood:	n/a	chr15:41096103-41096112
49	CTCF	chr15:41095960-41096110	HPAF	blood vessel:	n/a	n/a
50	CTCF	chr15:41096040-41096190	GM12870	blood:	n/a	chr15:41096103-41096112

No.	Distal block	Cell Line	Cell type
1	chr15:41094059..41097035-chr15:41107572..41109488,2	MCF-7	breast:
2	chr15:41092798..41096525-chr15:41096883..41100416,6	K562	blood:
3	chr15:41090711..41092456-chr15:41094333..41096481,2	K562	blood:
4	chr15:41095336..41097635-chr15:41142803..41144806,2	MCF-7	breast:
5	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

Variant related genes	Relation type
ZFYVE19	TF binding region
ENSG00000166145	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000166140	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10152371	0.89[JPT][hapmap]
rs11070294	0.81[EUR][1000 genomes]
rs17657877	0.89[JPT][hapmap]
rs2412567	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7178506	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs7178506	ZFYVE19	cis	multi-tissue	Pritchard
rs7178506	CCDC32	cis	multi-tissue	Pritchard
rs7178506	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41072600-41098600	Weak transcription	Fetal Brain Female	brain
2	chr15:41072600-41098600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:41078200-41098600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41079600-41098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41080000-41099000	Weak transcription	Aorta	Aorta
6	chr15:41080400-41098200	Weak transcription	GM12878-XiMat	blood
7	chr15:41080400-41098600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:41080400-41098800	Weak transcription	Brain Angular Gyrus	brain
9	chr15:41080400-41098800	Weak transcription	Brain Anterior Caudate	brain
10	chr15:41080600-41098200	Weak transcription	Fetal Thymus	thymus
11	chr15:41080600-41098600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:41080600-41098600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:41080600-41098600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:41081400-41098200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:41082000-41098600	Weak transcription	Fetal Lung	lung
16	chr15:41082000-41098800	Weak transcription	Fetal Kidney	kidney
17	chr15:41084400-41098200	Weak transcription	Brain Germinal Matrix	brain
18	chr15:41084800-41098200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:41086000-41098200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:41086000-41098600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:41086000-41098600	Weak transcription	Primary B cells from cord blood	blood
22	chr15:41086000-41098800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:41086000-41098800	Weak transcription	Esophagus	oesophagus
24	chr15:41086200-41098400	Weak transcription	K562	blood
25	chr15:41086200-41098600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:41086200-41098600	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:41086200-41098600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:41086200-41098600	Weak transcription	Brain Substantia Nigra	brain
29	chr15:41086200-41098600	Weak transcription	HSMM	muscle
30	chr15:41086200-41098600	Weak transcription	NH-A	brain
31	chr15:41086200-41098600	Weak transcription	Osteobl	bone
32	chr15:41086200-41098800	Weak transcription	HSMMtube	muscle
33	chr15:41086200-41098800	Weak transcription	NHDF-Ad	bronchial
34	chr15:41086400-41098600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:41087800-41098600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:41088600-41098200	Weak transcription	Adipose Nuclei	Adipose
37	chr15:41089200-41098200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr15:41089200-41098200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:41089200-41098200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr15:41089200-41098800	Weak transcription	Small Intestine	intestine
41	chr15:41089400-41098200	Weak transcription	Spleen	Spleen
42	chr15:41089400-41098600	Weak transcription	Colonic Mucosa	Colon
43	chr15:41089400-41098600	Weak transcription	HUVEC	blood vessel
44	chr15:41089600-41098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:41089600-41098800	Weak transcription	HMEC	breast
46	chr15:41090800-41097600	Strong transcription	Fetal Stomach	stomach
47	chr15:41091000-41098200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr15:41091000-41098600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:41091000-41098600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:41091000-41098600	Weak transcription	A549	lung

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