Variant report

Variant	rs12909221
Chromosome Location	chr15:45902779-45902780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45457952..45460656-chr15:45900362..45903240,2	K562	blood:

Variant related genes	Relation type
ENSG00000259539	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs4337250	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636910	0.81[JPT][hapmap]
rs950027	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12909221	BMF	cis	parietal	SCAN
rs12909221	SLC28A2	cis	cerebellum	SCAN
rs12909221	GATM	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45881000-45908600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:45881000-45908800	Weak transcription	Esophagus	oesophagus
3	chr15:45881200-45909000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:45881800-45903400	Weak transcription	Brain Substantia Nigra	brain
5	chr15:45881800-45904800	Weak transcription	NHEK	skin
6	chr15:45882000-45908600	Weak transcription	NHLF	lung
7	chr15:45888800-45904800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:45889000-45903600	Weak transcription	Thymus	Thymus
9	chr15:45889600-45906600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:45889800-45904800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:45889800-45905400	Weak transcription	Fetal Intestine Small	intestine
12	chr15:45889800-45908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:45890200-45908800	Weak transcription	A549	lung
14	chr15:45896600-45903000	Weak transcription	Spleen	Spleen
15	chr15:45896800-45912400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:45898000-45903000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:45898400-45911000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:45898800-45903600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:45898800-45903600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:45898800-45904600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:45898800-45906600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:45898800-45906600	Weak transcription	Pancreas	Pancrea
23	chr15:45898800-45909200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:45898800-45911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:45899000-45904800	Weak transcription	NH-A	brain
26	chr15:45899000-45906600	Weak transcription	HepG2	liver
27	chr15:45899200-45903200	Strong transcription	Fetal Stomach	stomach
28	chr15:45899400-45903200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:45899400-45904800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:45899400-45904800	Weak transcription	HSMM	muscle
31	chr15:45899400-45904800	Weak transcription	NHDF-Ad	bronchial
32	chr15:45899400-45906800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:45899400-45909000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:45899600-45903600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:45899600-45903600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:45899600-45903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:45899600-45904600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:45899600-45904800	Weak transcription	HUVEC	blood vessel
39	chr15:45899600-45904800	Weak transcription	Osteobl	bone
40	chr15:45899600-45906600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:45899600-45906800	Weak transcription	Brain Anterior Caudate	brain
42	chr15:45899600-45912400	Weak transcription	HSMMtube	muscle
43	chr15:45899800-45903000	Weak transcription	Left Ventricle	heart
44	chr15:45899800-45903200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:45899800-45903600	Weak transcription	Ovary	ovary
46	chr15:45899800-45905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:45899800-45906600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:45900000-45903800	Weak transcription	Fetal Thymus	thymus
49	chr15:45900200-45903800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:45900800-45903200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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