Variant report

Variant	rs12931879
Chromosome Location	chr16:47526819-47526820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:47525470..47528929-chr16:47529310..47531688,3	K562	blood:
2	chr16:47521997..47524877-chr16:47525537..47527944,2	K562	blood:
3	chr16:47497354..47500127-chr16:47526363..47529187,2	K562	blood:
4	chr16:47493908..47496119-chr16:47525530..47527640,2	K562	blood:
5	chr16:47516457..47520432-chr16:47524851..47526977,4	K562	blood:

Variant related genes	Relation type
ENSG00000102893	Chromatin interaction
ENSG00000129636	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1015543	1.00[JPT][hapmap]
rs11247408	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1137143	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11863453	0.95[ASN][1000 genomes]
rs1200995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12922960	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13332786	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13335733	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17739525	1.00[MEX][hapmap];0.86[TSI][hapmap]
rs35183491	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35514741	0.82[EUR][1000 genomes]
rs3809676	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	esv2758423	chr16:47316866-47606287	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv427983	chr16:47316866-47606287	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv533068	chr16:47354593-47559639	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv833217	chr16:47358148-47527655	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	esv34317	chr16:47390600-47672479	Weak transcription ZNF genes & repeats Enhancers Strong transcription 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	16 gene(s)	inside rSNPs	diseases
11	esv1822041	chr16:47399460-47569732	Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised 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	12 gene(s)	inside rSNPs	diseases
12	nsv572537	chr16:47411203-47599502	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv520355	chr16:47424828-48164777	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
14	esv1794084	chr16:47478207-47676184	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1059367	chr16:47524706-47586335	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv2761905	chr16:47524718-47586347	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12931879	PHKB	cis	parietal	SCAN
rs12931879	SLC15A4	trans	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47496200-47532000	Weak transcription	Ovary	ovary
2	chr16:47496200-47538400	Weak transcription	NH-A	brain
3	chr16:47498200-47527800	Weak transcription	Small Intestine	intestine
4	chr16:47502400-47533200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:47518800-47531600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr16:47519400-47527200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:47521000-47536400	Weak transcription	HSMMtube	muscle
8	chr16:47521400-47527000	ZNF genes & repeats	Liver	Liver
9	chr16:47524600-47545800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr16:47525200-47527000	Flanking Active TSS	GM12878-XiMat	blood
11	chr16:47525200-47533400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:47525400-47532600	Weak transcription	Fetal Heart	heart
13	chr16:47525600-47527200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
14	chr16:47525800-47527200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr16:47525800-47527200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr16:47525800-47527400	Enhancers	Dnd41	blood
17	chr16:47525800-47527600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr16:47525800-47528400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr16:47525800-47536800	Weak transcription	A549	lung
20	chr16:47525800-47538600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr16:47525800-47563000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr16:47526000-47527000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr16:47526000-47527000	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr16:47526000-47527200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr16:47526000-47527200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:47526000-47527200	Enhancers	Primary T cells fromperipheralblood	blood
27	chr16:47526000-47527200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr16:47526000-47527200	Enhancers	Left Ventricle	heart
29	chr16:47526000-47527200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr16:47526000-47527200	Enhancers	Spleen	Spleen
31	chr16:47526000-47527600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr16:47526200-47527000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr16:47526200-47527000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr16:47526200-47528600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr16:47526200-47529600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr16:47526200-47532000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:47526200-47537800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:47526400-47527000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr16:47526400-47527000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:47526400-47527000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr16:47526400-47527000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr16:47526400-47527000	Active TSS	Duodenum Mucosa	Duodenum
43	chr16:47526400-47527000	ZNF genes & repeats	Esophagus	oesophagus
44	chr16:47526400-47527000	Enhancers	Psoas Muscle	Psoas
45	chr16:47526400-47527000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr16:47526400-47527000	Flanking Active TSS	HepG2	liver
47	chr16:47526400-47527200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr16:47526400-47527200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr16:47526400-47527200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr16:47526400-47527200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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