Variant report

Variant	rs12051
Chromosome Location	chr17:46103760-46103761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46101739..46105145-chr17:46207358..46210173,3	MCF-7	breast:
2	chr17:46103207..46104778-chr17:46151389..46152380,11	K562	blood:
3	chr17:46101075..46105793-chr17:46203518..46208640,6	MCF-7	breast:
4	chr17:46101220..46105616-chr17:46211133..46214847,5	K562	blood:
5	chr17:46100290..46104941-chr17:46183793..46186470,6	MCF-7	breast:
6	chr17:46103502..46104385-chr17:46125648..46126403,3	K562	blood:
7	chr17:46102233..46104443-chr17:46148232..46151120,2	K562	blood:
8	chr17:46102704..46105485-chr17:46150295..46153343,3	MCF-7	breast:
9	chr17:45973640..45975276-chr17:46101393..46103848,2	MCF-7	breast:
10	chr17:46103657..46104374-chr17:46151449..46152362,3	MCF-7	breast:
11	chr17:46103505..46104454-chr17:46208306..46209160,6	K562	blood:
12	chr17:46037650..46039403-chr17:46103003..46105504,2	K562	blood:
13	chr17:46103659..46104450-chr17:46174735..46175375,2	MCF-7	breast:
14	chr17:46102745..46105471-chr17:46206069..46210163,5	K562	blood:
15	chr17:46103470..46105367-chr17:46151436..46152289,6	MCF-7	breast:
16	chr17:46102966..46105388-chr17:46145641..46147394,2	K562	blood:
17	chr17:46103474..46104130-chr17:46157398..46158242,2	MCF-7	breast:
18	chr17:46044123..46046243-chr17:46103230..46105369,2	MCF-7	breast:
19	chr17:46100592..46104586-chr17:46183324..46186520,4	K562	blood:
20	chr17:46102851..46105550-chr17:46199872..46202014,2	MCF-7	breast:
21	chr17:46103492..46104374-chr9:83452149..83452649,2	MCF-7	breast:
22	chr17:46101312..46103922-chr17:46212522..46214057,2	MCF-7	breast:
23	chr17:46103422..46105528-chr17:46131002..46133417,2	K562	blood:
24	chr17:46047240..46049948-chr17:46101636..46104344,3	MCF-7	breast:
25	chr11:62607625..62609532-chr17:46102709..46105025,2	K562	blood:
26	chr17:46033388..46035885-chr17:46101144..46103907,2	MCF-7	breast:
27	chr17:46101261..46104972-chr17:46659979..46662985,3	K562	blood:
28	chr17:46103572..46104350-chr17:46208345..46209728,6	MCF-7	breast:
29	chr17:46102299..46104272-chr17:46156219..46158747,2	MCF-7	breast:
30	chr17:46102851..46105314-chr17:46237154..46238995,2	MCF-7	breast:
31	chr17:46070659..46072225-chr17:46102465..46104720,2	K562	blood:
32	chr17:46101351..46104299-chr17:46183324..46186063,2	K562	blood:
33	chr17:46101917..46105138-chr17:46176105..46179935,5	K562	blood:
34	chr17:46046874..46048813-chr17:46100923..46104280,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPZ2-2	chr17:46103537-46103841	NONHSAT054364

No data

Variant related genes	Relation type
ENSG00000108468	Chromatin interaction
ENSG00000141293	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000120093	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10491182	0.84[YRI][hapmap]
rs10491183	0.84[YRI][hapmap]
rs11651275	0.95[YRI][hapmap]
rs12601350	0.94[ASN][1000 genomes]
rs12602131	0.94[ASN][1000 genomes]
rs12602670	0.98[ASN][1000 genomes]
rs1473117	0.93[ASN][1000 genomes]
rs2240119	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs41429650	0.89[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs58554000	0.93[ASN][1000 genomes]
rs7209072	0.84[YRI][hapmap]
rs72823528	0.98[ASN][1000 genomes]
rs72823532	0.98[ASN][1000 genomes]
rs72823533	0.94[ASN][1000 genomes]
rs757353	0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs9898218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903963	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12051	G6PC	cis	parietal	SCAN
rs12051	PNPO	cis	cerebellum	SCAN
rs12051	PNPO	cis	parietal	SCAN
rs12051	ATXN7L3	cis	cerebellum	SCAN
rs12051	HOXB6	cis	cerebellum	SCAN
rs12051	NFE2L1	cis	cerebellum	SCAN
rs12051	OSBPL7	cis	cerebellum	SCAN
rs12051	C17orf57	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46100400-46103800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:46101400-46104200	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr17:46102600-46104600	Enhancers	Stomach Mucosa	stomach
4	chr17:46102800-46103800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
5	chr17:46102800-46103800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:46102800-46103800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:46102800-46103800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:46102800-46103800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr17:46102800-46103800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr17:46102800-46103800	Flanking Active TSS	NH-A	brain
11	chr17:46102800-46104000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:46102800-46104200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:46102800-46104400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:46102800-46104400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr17:46102800-46104400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr17:46102800-46104400	Flanking Active TSS	NHEK	skin
17	chr17:46102800-46104400	Flanking Active TSS	Osteobl	bone
18	chr17:46102800-46104600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:46102800-46104600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:46102800-46104600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr17:46102800-46104600	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr17:46103000-46103800	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr17:46103000-46103800	Flanking Active TSS	NHLF	lung
24	chr17:46103000-46104400	Enhancers	Lung	lung
25	chr17:46103000-46104400	Flanking Active TSS	A549	lung
26	chr17:46103000-46104600	Flanking Active TSS	Hela-S3	cervix
27	chr17:46103200-46103800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:46103200-46103800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:46103200-46103800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:46103200-46104000	Enhancers	Primary B cells from cord blood	blood
31	chr17:46103200-46104000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr17:46103200-46104000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr17:46103200-46104000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr17:46103200-46104000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:46103200-46104200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr17:46103200-46104200	Enhancers	Primary hematopoietic stem cells	blood
37	chr17:46103200-46104200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr17:46103200-46104200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:46103200-46104200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr17:46103200-46104200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr17:46103200-46104200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:46103200-46104200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:46103200-46104200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:46103200-46104200	Enhancers	Dnd41	blood
45	chr17:46103200-46104400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:46103200-46104400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:46103200-46104400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
48	chr17:46103200-46104400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
49	chr17:46103200-46104400	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr17:46103200-46104400	Enhancers	Primary B cells from peripheral blood	blood

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