Variant report

Variant	rs12362406
Chromosome Location	chr11:57550785-57550786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57545406..57547871-chr11:57550321..57552770,3	MCF-7	breast:
2	chr11:57529135..57533999-chr11:57544009..57550841,10	MCF-7	breast:
3	chr11:57528048..57531097-chr11:57548778..57551270,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198561	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12365669	0.88[ASN][1000 genomes]
rs12801694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278108	1.00[LWK][hapmap]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer 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	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12362406	TIMM10	cis	Heart Left Ventricle	GTEx
rs12362406	YPEL4	cis	lung	GTEx
rs12362406	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs12362406	TIMM10	cis	multi-tissue	Pritchard
rs12362406	YPEL4	cis	multi-tissue	Pritchard
rs12362406	TIMM10	cis	Artery Tibial	GTEx
rs12362406	TIMM10	cis	parietal	SCAN
rs12362406	OR5W2	cis	parietal	SCAN
rs12362406	OR5T3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57539600-57552000	Enhancers	Placenta	Placenta
2	chr11:57543000-57551200	Enhancers	Pancreas	Pancrea
3	chr11:57545200-57551600	Weak transcription	Gastric	stomach
4	chr11:57545200-57555400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:57546400-57559000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:57546400-57559200	Enhancers	Stomach Mucosa	stomach
7	chr11:57546600-57554000	Genic enhancers	Fetal Intestine Small	intestine
8	chr11:57546800-57551000	Enhancers	Right Ventricle	heart
9	chr11:57546800-57554800	Weak transcription	Fetal Brain Female	brain
10	chr11:57546800-57564000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:57547000-57555400	Enhancers	Duodenum Mucosa	Duodenum
12	chr11:57547000-57558600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:57547000-57558600	Enhancers	Liver	Liver
14	chr11:57547200-57550800	Enhancers	Fetal Heart	heart
15	chr11:57547200-57552000	Enhancers	Brain Angular Gyrus	brain
16	chr11:57547200-57552400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:57547200-57552800	Weak transcription	Dnd41	blood
18	chr11:57547200-57555200	Weak transcription	Fetal Brain Male	brain
19	chr11:57547200-57555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:57547400-57554000	Weak transcription	Osteobl	bone
21	chr11:57547400-57555000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:57547400-57555000	Weak transcription	Brain Germinal Matrix	brain
23	chr11:57547400-57558600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr11:57547400-57558800	Weak transcription	Aorta	Aorta
25	chr11:57547800-57550800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:57547800-57554200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:57547800-57558600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:57548000-57550800	Genic enhancers	HepG2	liver
29	chr11:57548000-57551200	Weak transcription	GM12878-XiMat	blood
30	chr11:57548000-57554200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:57548400-57554000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:57548400-57554400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr11:57549000-57555000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:57549200-57550800	Enhancers	Left Ventricle	heart
35	chr11:57549200-57551400	Enhancers	A549	lung
36	chr11:57549200-57557200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr11:57549400-57551400	Weak transcription	Right Atrium	heart
38	chr11:57549400-57553800	Weak transcription	Fetal Stomach	stomach
39	chr11:57549400-57554000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr11:57549400-57554200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:57549400-57554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:57549400-57554400	Weak transcription	NHLF	lung
43	chr11:57549400-57555000	Weak transcription	Spleen	Spleen
44	chr11:57549400-57555800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:57549400-57558400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:57549400-57559600	Weak transcription	Hela-S3	cervix
47	chr11:57549600-57552000	Weak transcription	Primary B cells from cord blood	blood
48	chr11:57549600-57552400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:57549600-57554200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:57549600-57554400	Weak transcription	HSMM	muscle

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