Variant report

Variant	rs56886112
Chromosome Location	chr15:41092200-41092201
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41090711..41092456-chr15:41094333..41096481,2	K562	blood:
2	chr15:41091715..41095520-chr15:41097654..41103176,7	K562	blood:
3	chr15:41090706..41092456-chr15:41094333..41095842,2	K562	blood:
4	chr15:41086302..41089944-chr15:41090319..41093510,4	K562	blood:
5	chr15:41055763..41058275-chr15:41091968..41094826,2	K562	blood:

Variant related genes	Relation type
ENSG00000166140	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000137880	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11070294	0.89[EUR][1000 genomes]
rs11070295	0.88[EUR][1000 genomes]
rs11070296	0.88[EUR][1000 genomes]
rs11070297	0.81[EUR][1000 genomes]
rs11855641	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856866	0.86[EUR][1000 genomes]
rs11858010	0.81[EUR][1000 genomes]
rs12148058	0.87[EUR][1000 genomes]
rs12909824	0.88[EUR][1000 genomes]
rs12916485	0.87[EUR][1000 genomes]
rs2010300	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289219	0.85[EUR][1000 genomes]
rs2899000	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34143869	0.86[EUR][1000 genomes]
rs34621344	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35458726	0.88[EUR][1000 genomes]
rs35621205	0.85[EUR][1000 genomes]
rs3736286	0.87[EUR][1000 genomes]
rs3743033	0.88[EUR][1000 genomes]
rs3743034	0.80[EUR][1000 genomes]
rs4402538	0.87[EUR][1000 genomes]
rs57818172	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57825040	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57943888	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57994257	0.88[EUR][1000 genomes]
rs62018584	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62018585	0.81[EUR][1000 genomes]
rs6492967	0.85[EUR][1000 genomes]
rs745032	0.87[EUR][1000 genomes]
rs8037830	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs56886112	C15orf57	cis	Adipose Subcutaneous	GTEx
rs56886112	CCDC32	cis	multi-tissue	Pritchard
rs56886112	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs56886112	ZFYVE19	cis	multi-tissue	Pritchard
rs56886112	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs56886112	C15orf57	cis	Artery Tibial	GTEx
rs56886112	C15orf57	cis	Esophagus Muscularis	GTEx
rs56886112	C15orf57	cis	lung	GTEx
rs56886112	RP11-111A22.1	cis	lung	GTEx
rs56886112	ZFYVE19	cis	Artery Tibial	GTEx
rs56886112	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs56886112	RP11-111A22.1	cis	Artery Tibial	GTEx

Chromatin state (count:117 , 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	chr15:41080000-41094600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:41080000-41099000	Weak transcription	Aorta	Aorta
7	chr15:41080400-41093000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:41080400-41098200	Weak transcription	GM12878-XiMat	blood
9	chr15:41080400-41098600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:41080400-41098800	Weak transcription	Brain Angular Gyrus	brain
11	chr15:41080400-41098800	Weak transcription	Brain Anterior Caudate	brain
12	chr15:41080600-41098200	Weak transcription	Fetal Thymus	thymus
13	chr15:41080600-41098600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:41080600-41098600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:41080600-41098600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:41081400-41098200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:41081800-41094600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:41081800-41094600	Weak transcription	Ovary	ovary
19	chr15:41082000-41095000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:41082000-41096000	Weak transcription	Dnd41	blood
21	chr15:41082000-41098600	Weak transcription	Fetal Lung	lung
22	chr15:41082000-41098800	Weak transcription	Fetal Kidney	kidney
23	chr15:41083200-41093400	Weak transcription	Thymus	Thymus
24	chr15:41084400-41098200	Weak transcription	Brain Germinal Matrix	brain
25	chr15:41084800-41095600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:41084800-41098200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:41085000-41094800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:41085200-41095400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:41085600-41093200	Weak transcription	Placenta	Placenta
30	chr15:41085800-41095400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:41086000-41093200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:41086000-41094000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:41086000-41094200	Weak transcription	Right Atrium	heart
34	chr15:41086000-41095200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:41086000-41098200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:41086000-41098600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:41086000-41098600	Weak transcription	Primary B cells from cord blood	blood
38	chr15:41086000-41098800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:41086000-41098800	Weak transcription	Esophagus	oesophagus
40	chr15:41086200-41093200	Weak transcription	Primary T cells from cord blood	blood
41	chr15:41086200-41094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:41086200-41094600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:41086200-41094600	Weak transcription	NHLF	lung
44	chr15:41086200-41098400	Weak transcription	K562	blood
45	chr15:41086200-41098600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:41086200-41098600	Weak transcription	Brain Hippocampus Middle	brain
47	chr15:41086200-41098600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:41086200-41098600	Weak transcription	Brain Substantia Nigra	brain
49	chr15:41086200-41098600	Weak transcription	HSMM	muscle
50	chr15:41086200-41098600	Weak transcription	NH-A	brain

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