Variant report

Variant	rs12928230
Chromosome Location	chr16:47303838-47303839
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	chr16:47290686..47293346-chr16:47302878..47305751,2	K562	blood:
2	chr16:47298562..47302472-chr16:47302634..47305844,3	K562	blood:

Variant related genes	Relation type
ENSG00000129636	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12920194	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs174642	1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2880117	0.84[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs34396829	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs34397861	0.85[AFR][1000 genomes]
rs3809676	0.84[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1795199	chr16:47111119-47732476	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1803802	chr16:47115776-47367144	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv906660	chr16:47123724-47347780	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1059763	chr16:47147194-47373834	ZNF genes & repeats Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv528423	chr16:47163874-47347780	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv1821100	chr16:47171333-47330244	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	esv1821089	chr16:47223418-47330244	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv1832105	chr16:47223418-47347780	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv916572	chr16:47227786-47646103	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv933151	chr16:47236330-47646103	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
13	esv2757637	chr16:47261512-47595005	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 target site	16 gene(s)	inside rSNPs	diseases
14	esv2758644	chr16:47261512-47606287	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv1060396	chr16:47264261-47469345	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12928230	PHKB	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47230000-47332600	Weak transcription	Thymus	Thymus
2	chr16:47264200-47321000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr16:47282200-47321000	Weak transcription	Brain Hippocampus Middle	brain
4	chr16:47282400-47305000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr16:47285200-47305000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:47289200-47320600	Weak transcription	Small Intestine	intestine
7	chr16:47291800-47305800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr16:47291800-47306200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:47292200-47317400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr16:47292200-47345600	Weak transcription	K562	blood
11	chr16:47292400-47308600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr16:47292400-47317400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:47292400-47317400	Weak transcription	HSMM	muscle
14	chr16:47292600-47306800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr16:47292600-47316600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:47292600-47317200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr16:47292600-47317200	Weak transcription	Dnd41	blood
18	chr16:47292600-47317200	Weak transcription	HepG2	liver
19	chr16:47294600-47319600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr16:47294600-47332600	Weak transcription	Pancreas	Pancrea
21	chr16:47294800-47306000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr16:47294800-47332600	Weak transcription	Ovary	ovary
23	chr16:47295200-47317200	Weak transcription	Liver	Liver
24	chr16:47295200-47317400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr16:47297400-47304400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr16:47297400-47314600	Weak transcription	Aorta	Aorta
27	chr16:47297400-47317200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:47297400-47317200	Weak transcription	Adipose Nuclei	Adipose
29	chr16:47297400-47317200	Weak transcription	Left Ventricle	heart
30	chr16:47297400-47319000	Weak transcription	Fetal Stomach	stomach
31	chr16:47297400-47319400	Weak transcription	Lung	lung
32	chr16:47297600-47304000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr16:47297600-47304400	Weak transcription	Primary B cells from cord blood	blood
34	chr16:47297600-47305200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr16:47297600-47317200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr16:47297600-47317400	Weak transcription	Fetal Intestine Large	intestine
37	chr16:47297600-47333200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr16:47297800-47316600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr16:47303600-47305000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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