Variant report

Variant	rs1411153
Chromosome Location	chr9:18363377-18363378
allele	A/C
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	TCF12	chr9:18363237-18363905	SK-N-SH	brain:	n/a	chr9:18363310-18363319
2	GATA3	chr9:18363207-18363868	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr9:18363050-18363823	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr9:18363092-18363964	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr9:18363308-18363850	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000227167	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10511651	0.85[EUR][1000 genomes]
rs11790709	0.87[EUR][1000 genomes]
rs1340046	0.86[AFR][1000 genomes]
rs1417040	0.85[EUR][1000 genomes]
rs1417041	0.86[AFR][1000 genomes]
rs17202635	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17202704	0.94[EUR][1000 genomes]
rs17791761	1.00[CEU][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs17792334	0.84[EUR][1000 genomes]
rs17792440	0.82[EUR][1000 genomes]
rs1854548	0.81[AFR][1000 genomes]
rs2226018	0.85[EUR][1000 genomes]
rs4961464	0.83[AFR][1000 genomes]
rs56790980	0.85[EUR][1000 genomes]
rs7028195	0.82[AFR][1000 genomes]
rs9407898	0.86[AFR][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	nsv831522	chr9:18231982-18459492	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2764161	chr9:18247433-18443060	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892684	chr9:18261485-18401585	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS 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	9 gene(s)	inside rSNPs	diseases
6	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv892687	chr9:18303691-18430297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv1831194	chr9:18355044-18369216	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1411153	MLLT3	cis	parietal	SCAN
rs1411153	IFNA14	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18333400-18368200	Weak transcription	Aorta	Aorta
2	chr9:18357400-18364200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:18358000-18364200	Enhancers	NHDF-Ad	bronchial
4	chr9:18358000-18364400	Enhancers	Osteobl	bone
5	chr9:18360000-18364000	Enhancers	Fetal Lung	lung
6	chr9:18361600-18364200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:18361600-18368400	Weak transcription	HUVEC	blood vessel
8	chr9:18362200-18363400	Weak transcription	Fetal Kidney	kidney
9	chr9:18362400-18364000	Enhancers	Colon Smooth Muscle	Colon
10	chr9:18362400-18364000	Enhancers	HSMM	muscle
11	chr9:18362400-18364200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:18362400-18364400	Enhancers	Fetal Stomach	stomach
13	chr9:18362600-18363600	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:18362600-18367400	Enhancers	Primary B cells from cord blood	blood
15	chr9:18362800-18363400	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr9:18362800-18363400	Enhancers	GM12878-XiMat	blood
17	chr9:18362800-18363800	Enhancers	NH-A	brain
18	chr9:18362800-18364200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:18362800-18364200	Enhancers	Rectal Smooth Muscle	rectum
20	chr9:18363000-18363400	Enhancers	Pancreas	Pancrea
21	chr9:18363000-18363600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:18363000-18363800	Enhancers	HSMMtube	muscle
23	chr9:18363000-18364000	Enhancers	Stomach Smooth Muscle	stomach
24	chr9:18363000-18364200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:18363000-18364200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr9:18363000-18364200	Enhancers	NHLF	lung
27	chr9:18363000-18366600	Enhancers	Fetal Heart	heart
28	chr9:18363200-18363400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:18363200-18363400	Enhancers	Left Ventricle	heart
30	chr9:18363200-18363400	Enhancers	Psoas Muscle	Psoas
31	chr9:18363200-18363800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:18363200-18364000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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