Variant report

Variant	rs16928163
Chromosome Location	chr12:25047720-25047721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:25046064..25048291-chr12:25061762..25064240,2	K562	blood:
2	chr12:25045934..25049646-chr12:25051521..25056229,4	K562	blood:
3	chr12:25047299..25050806-chr12:25051521..25055425,5	K562	blood:

Variant related genes	Relation type
ENSG00000060982	Chromatin interaction
ENSG00000268865	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11047684	0.80[AMR][1000 genomes]
rs11047685	0.80[AMR][1000 genomes]
rs11047689	0.81[CHD][hapmap]
rs11047693	0.92[CHB][hapmap];0.87[CHD][hapmap];0.92[ASN][1000 genomes]
rs12296255	0.80[AMR][1000 genomes]
rs12302883	0.80[AMR][1000 genomes]
rs12310054	0.80[AMR][1000 genomes]
rs12316475	0.82[AMR][1000 genomes]
rs12319639	0.80[AMR][1000 genomes]
rs12425320	0.80[AMR][1000 genomes]
rs2062497	0.80[AMR][1000 genomes]
rs2270771	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2270772	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143211	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4143212	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs60686976	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7136511	0.85[EUR][1000 genomes]
rs73061850	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7307610	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1053309	chr12:24770995-25078227	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
13	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
14	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv1045302	chr12:24921100-25078227	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
17	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	13 gene(s)	inside rSNPs	diseases
18	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1054863	chr12:24941350-25078227	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
20	nsv541426	chr12:24941350-25078227	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
21	nsv1051968	chr12:24941350-25138118	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	nsv541427	chr12:24941350-25138118	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
24	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
25	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16928163	BCAT1	cis	multi-tissue	Pritchard
rs16928163	ARNTL2	cis	parietal	SCAN
rs16928163	SLCO1B1	cis	parietal	SCAN
rs16928163	PPFIBP1	cis	parietal	SCAN
rs16928163	MED21	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24971000-25054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:24992000-25053000	Weak transcription	Fetal Stomach	stomach
3	chr12:24992600-25053400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:25015600-25055200	Weak transcription	Aorta	Aorta
5	chr12:25018400-25054600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:25020200-25054800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:25022200-25053400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:25022400-25051400	Weak transcription	Lung	lung
9	chr12:25023000-25053000	Weak transcription	GM12878-XiMat	blood
10	chr12:25024200-25053600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:25026000-25048000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:25030600-25048000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:25031000-25049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:25031000-25054000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:25031200-25063600	Weak transcription	HepG2	liver
16	chr12:25031400-25054000	Weak transcription	Fetal Brain Female	brain
17	chr12:25031600-25053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:25035000-25054600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:25035200-25053400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:25038600-25048000	Weak transcription	Adipose Nuclei	Adipose
21	chr12:25039000-25051400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:25039400-25054800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:25040200-25051400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:25041600-25048200	Strong transcription	HSMM	muscle
25	chr12:25041600-25052400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:25041800-25048000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:25042400-25048200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr12:25042400-25053400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:25042800-25051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:25043000-25053800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:25043000-25054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:25043200-25053400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:25043400-25054800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:25043600-25047800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:25043800-25048200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:25043800-25048200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:25044200-25048000	Weak transcription	Pancreas	Pancrea
38	chr12:25044400-25054800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:25045000-25050000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:25045400-25048200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:25045800-25047800	Weak transcription	HSMMtube	muscle
42	chr12:25045800-25048000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:25045800-25053800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:25045800-25054800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr12:25046000-25054200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:25046400-25054800	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:25047200-25048000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:25047200-25048200	Enhancers	Brain Cingulate Gyrus	brain
49	chr12:25047200-25048400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:25047200-25048400	Enhancers	Fetal Kidney	kidney

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