Variant report

Variant	rs1117050
Chromosome Location	chr11:34926338-34926339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34921303..34922935-chr11:34924601..34927346,2	MCF-7	breast:
2	chr11:34923546..34926678-chr11:34933429..34938581,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149089	Chromatin interaction
ENSG00000110435	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10488802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10836317	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11539202	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11601737	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11602364	0.82[AMR][1000 genomes]
rs11602584	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11605600	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11605972	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11605993	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11606580	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11606871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11607986	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11608116	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1409718	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17347979	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17348697	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17348711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17349298	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17363135	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17432226	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17433496	0.96[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17434808	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17434946	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17711539	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17783998	0.82[AMR][1000 genomes]
rs17784324	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2217479	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3852515	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3852516	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3852517	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4534556	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55672020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55868872	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55911702	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55929026	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55957800	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56061305	0.83[EUR][1000 genomes]
rs61734605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7110461	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72912924	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72912934	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72914758	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72922479	0.82[AMR][1000 genomes]
rs72922482	0.82[AMR][1000 genomes]
rs72924508	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72924541	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72924562	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72926580	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72928507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930462	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72930468	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72930480	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7479823	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7937316	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7948977	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7950996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv8807	chr11:34912167-34930289	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv2757436	chr11:34913315-34963728	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
5	esv2759817	chr11:34913315-34963728	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
6	esv34511	chr11:34914124-34942836	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	esv2756165	chr11:34914137-34942836	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1117050	APIP	cis	Esophagus Muscularis	GTEx
rs1117050	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs1117050	APIP	cis	Adipose Subcutaneous	GTEx
rs1117050	APIP	cis	Artery Tibial	GTEx
rs1117050	APIP	cis	cerebellum	SCAN
rs1117050	APIP	cis	Thyroid	GTEx
rs1117050	APIP	cis	Nerve Tibial	GTEx
rs1117050	APIP	cis	Artery Aorta	GTEx
rs1117050	APIP	cis	Heart Left Ventricle	GTEx
rs1117050	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs1117050	APIP	cis	lung	GTEx
rs1117050	APIP	cis	Stomach	GTEx
rs1117050	PDHX	cis	cerebellum	SCAN
rs1117050	PDHX	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34898200-34926800	Weak transcription	HSMMtube	muscle
2	chr11:34913600-34929800	Weak transcription	K562	blood
3	chr11:34917600-34931000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:34918200-34928600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr11:34920000-34935800	Weak transcription	Fetal Heart	heart
6	chr11:34920800-34926400	ZNF genes & repeats	Dnd41	blood
7	chr11:34922000-34926800	Weak transcription	Aorta	Aorta
8	chr11:34922400-34936600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:34922400-34936600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:34922600-34936200	Weak transcription	Right Ventricle	heart
11	chr11:34922600-34936600	Weak transcription	NHEK	skin
12	chr11:34922800-34928600	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr11:34922800-34936600	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:34923000-34929800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:34923000-34930200	ZNF genes & repeats	Fetal Brain Female	brain
16	chr11:34923000-34930400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:34923000-34931000	Weak transcription	Gastric	stomach
18	chr11:34923000-34931000	Weak transcription	Lung	lung
19	chr11:34923000-34934600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:34923000-34934600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:34923000-34936000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr11:34923000-34936800	Weak transcription	Colonic Mucosa	Colon
23	chr11:34923200-34926400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:34923200-34936600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:34923200-34936600	Weak transcription	NHLF	lung
26	chr11:34923400-34930000	Weak transcription	Brain Substantia Nigra	brain
27	chr11:34923400-34935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:34923400-34935200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:34923600-34930000	Weak transcription	Pancreas	Pancrea
30	chr11:34923600-34935200	Weak transcription	NHDF-Ad	bronchial
31	chr11:34923600-34936200	Weak transcription	Fetal Intestine Large	intestine
32	chr11:34923600-34937200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:34923800-34930000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:34923800-34932200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:34924000-34931000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr11:34924200-34932400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:34924200-34936200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr11:34924400-34928600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:34924600-34926800	Weak transcription	Psoas Muscle	Psoas
40	chr11:34924600-34931000	Weak transcription	Placenta	Placenta
41	chr11:34924800-34926800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:34924800-34931000	Weak transcription	Fetal Stomach	stomach
43	chr11:34925000-34926400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:34925000-34928600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:34925000-34928800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:34925000-34929800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:34925000-34936600	Weak transcription	Fetal Kidney	kidney
48	chr11:34925000-34937000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:34925200-34927000	Weak transcription	Thymus	Thymus
50	chr11:34925200-34929800	Weak transcription	A549	lung

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