Variant report

Variant	rs12423645
Chromosome Location	chr12:48143978-48143979
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	chr12:48136735..48141051-chr12:48142699..48146079,6	K562	blood:
2	chr12:48140978..48143189-chr12:48143371..48145379,2	K562	blood:

Variant related genes	Relation type
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12422983	1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12424297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426774	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12810487	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs12815308	1.00[JPT][hapmap]
rs12815462	0.84[AMR][1000 genomes]
rs12817548	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818212	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818241	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs4340112	1.00[JPT][hapmap]

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	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12423645	RAPGEF3	cis	Nerve Tibial	GTEx
rs12423645	RAPGEF3	cis	Thyroid	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
4	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
7	chr12:48135000-48145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
9	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:48135800-48145400	Weak transcription	NHDF-Ad	bronchial
12	chr12:48136000-48146200	Weak transcription	Osteobl	bone
13	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:48137800-48145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:48138000-48144200	Weak transcription	Pancreas	Pancrea
16	chr12:48138000-48148000	Weak transcription	Liver	Liver
17	chr12:48138400-48146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:48139400-48145200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:48139400-48146000	Weak transcription	Right Atrium	heart
20	chr12:48139400-48147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:48139600-48144200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:48139600-48145200	Strong transcription	Lung	lung
23	chr12:48139800-48144000	Strong transcription	Ovary	ovary
24	chr12:48139800-48144200	Strong transcription	Adipose Nuclei	Adipose
25	chr12:48139800-48146600	Weak transcription	Fetal Lung	lung
26	chr12:48139800-48146800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:48140000-48145400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr12:48140200-48144600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr12:48140200-48145200	Strong transcription	Brain Hippocampus Middle	brain
30	chr12:48140200-48145400	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr12:48140200-48145600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:48140200-48145600	Strong transcription	Brain Substantia Nigra	brain
33	chr12:48140200-48146200	Strong transcription	Fetal Stomach	stomach
34	chr12:48140200-48146800	Weak transcription	Fetal Heart	heart
35	chr12:48140400-48144200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr12:48140400-48144200	Strong transcription	Placenta	Placenta
37	chr12:48140400-48144600	Strong transcription	Esophagus	oesophagus
38	chr12:48140600-48145600	Strong transcription	Brain Anterior Caudate	brain
39	chr12:48140600-48145600	Strong transcription	HUVEC	blood vessel
40	chr12:48140800-48145400	Strong transcription	Brain Angular Gyrus	brain
41	chr12:48140800-48146000	Weak transcription	Stomach Mucosa	stomach
42	chr12:48141000-48145200	Strong transcription	Gastric	stomach
43	chr12:48141000-48145800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:48141200-48146000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:48141200-48147600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:48141600-48144800	Strong transcription	Fetal Kidney	kidney
47	chr12:48141600-48147000	Weak transcription	GM12878-XiMat	blood
48	chr12:48141800-48147000	Weak transcription	Primary B cells from cord blood	blood
49	chr12:48142000-48144000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:48142000-48145600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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