Variant report

Variant	rs12338528
Chromosome Location	chr9:96937989-96937990
allele	A/G
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	POLR2A	chr9:96937837-96938037	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr9:96937892-96938326	GM12878	blood:	n/a	n/a
3	POLR2A	chr9:96937965-96938356	GM12892	blood:	n/a	n/a
4	POLR2A	chr9:96935497-96946284	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:96936308-96938456	K562	blood:	n/a	n/a
6	GATA2	chr9:96937599-96938387	HUVEC	blood vessel:	n/a	chr9:96938123-96938144 chr9:96938125-96938139 chr9:96937599-96937609 chr9:96938129-96938139 chr9:96938030-96938040 chr9:96938126-96938142
7	POLR2A	chr9:96937836-96938516	HUVEC	blood vessel:	n/a	n/a
8	SPI1	chr9:96937927-96938127	GM12878	blood:	n/a	chr9:96938033-96938042
9	POLR2A	chr9:96935486-96946923	K562	blood:	n/a	n/a
10	POLR2A	chr9:96937967-96938123	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr9:96935500-96945447	A549	lung:	n/a	n/a
12	POLR2A	chr9:96937965-96938482	GM12892	blood:	n/a	n/a
13	SPI1	chr9:96937621-96938424	GM12878	blood:	n/a	chr9:96938033-96938042
14	RUNX3	chr9:96937866-96938275	GM12878	blood:	n/a	n/a
15	SPI1	chr9:96937876-96938235	GM12891	blood:	n/a	chr9:96938033-96938042
16	FOS	chr9:96937838-96938441	HUVEC	blood vessel:	n/a	n/a
17	RUNX3	chr9:96937743-96938383	GM12878	blood:	n/a	n/a
18	SPI1	chr9:96937873-96938260	GM12891	blood:	n/a	chr9:96938033-96938042
19	POLR2A	chr9:96937775-96940483	U87	brain:	n/a	n/a
20	IKZF1	chr9:96937892-96938315	GM12878	blood:	n/a	n/a
21	SPI1	chr9:96937911-96938187	GM12878	blood:	n/a	chr9:96938033-96938042
22	POLR2A	chr9:96937842-96938639	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96844456..96848566-chr9:96937566..96941042,3	K562	blood:
2	chr9:96791676..96794493-chr9:96936767..96941836,4	MCF-7	breast:
3	chr9:96790406..96793524-chr9:96937356..96939962,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269929	TF binding region
MIRLET7A1	TF binding region
MIRLET7D	TF binding region
MIRLET7F1	TF binding region
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10081759	1.00[EUR][1000 genomes]
rs10116369	1.00[EUR][1000 genomes]
rs10116630	1.00[EUR][1000 genomes]
rs10123498	1.00[EUR][1000 genomes]
rs12335636	1.00[EUR][1000 genomes]
rs12341848	1.00[EUR][1000 genomes]
rs12345658	1.00[EUR][1000 genomes]
rs28493183	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479531	1.00[EUR][1000 genomes]
rs7036037	1.00[EUR][1000 genomes]
rs7046683	1.00[EUR][1000 genomes]
rs7851345	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS 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	195 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12338528	HIATL1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96929600-96938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:96929800-96944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:96930400-96938200	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr9:96930600-96943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:96930600-96943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:96931200-96938200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr9:96931200-96938800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:96931800-96939000	Weak transcription	Fetal Brain Male	brain
11	chr9:96932000-96938200	Enhancers	Brain Anterior Caudate	brain
12	chr9:96932400-96938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:96933400-96939000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:96933600-96939400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:96933600-96939800	Strong transcription	Hela-S3	cervix
16	chr9:96933800-96940400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:96934000-96938200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr9:96934000-96941800	Strong transcription	Dnd41	blood
19	chr9:96934200-96939600	Enhancers	Brain Substantia Nigra	brain
20	chr9:96934200-96939800	Genic enhancers	Osteobl	bone
21	chr9:96934200-96941000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:96934400-96939800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:96934400-96942400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:96934600-96938400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr9:96934800-96938200	Weak transcription	Fetal Brain Female	brain
26	chr9:96934800-96938200	Genic enhancers	NHDF-Ad	bronchial
27	chr9:96935000-96938200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr9:96935000-96939600	Genic enhancers	HUVEC	blood vessel
29	chr9:96935000-96939800	Genic enhancers	A549	lung
30	chr9:96935200-96940600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:96935400-96938000	Strong transcription	Fetal Intestine Large	intestine
32	chr9:96935400-96938400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
33	chr9:96935400-96939200	Genic enhancers	NH-A	brain
34	chr9:96935400-96939400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:96935400-96939600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:96935400-96940000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:96935400-96940000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr9:96935400-96942200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:96935400-96942400	Strong transcription	Fetal Thymus	thymus
40	chr9:96935600-96938600	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr9:96935600-96939200	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr9:96935600-96939400	Genic enhancers	Liver	Liver
43	chr9:96935600-96942400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:96935600-96942400	Genic enhancers	HepG2	liver
45	chr9:96935800-96938400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr9:96935800-96938600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:96935800-96939200	Genic enhancers	HSMM	muscle
48	chr9:96935800-96939200	Genic enhancers	NHEK	skin
49	chr9:96935800-96940000	Strong transcription	K562	blood
50	chr9:96935800-96940400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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