Variant report

Variant	rs473465
Chromosome Location	chr12:57851182-57851183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57851169-57851437	HepG2	liver:	n/a	n/a
2	CTCF	chr12:57848200-57851732	A549	lung:	n/a	chr12:57849041-57849048 chr12:57848972-57848985
3	POLR2A	chr12:57851015-57851246	K562	blood:	n/a	n/a
4	EBF1	chr12:57851045-57851239	GM12878	blood:	n/a	chr12:57851187-57851198
5	RPC155	chr12:57851045-57851677	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57687373..57690350-chr12:57849601..57852128,3	K562	blood:
2	chr12:57849885..57859254-chr12:57908711..57915821,16	K562	blood:
3	chr12:57851014..57853081-chr12:57861682..57863559,2	K562	blood:
4	chr12:57622711..57625468-chr12:57850226..57853031,2	K562	blood:
5	chr12:57850914..57853325-chr12:57864861..57866988,3	K562	blood:
6	chr12:57843448..57846710-chr12:57847033..57851571,4	MCF-7	breast:
7	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:
8	chr12:57635862..57639345-chr12:57850429..57852757,3	K562	blood:
9	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
10	chr12:57828377..57830991-chr12:57850273..57852254,2	K562	blood:
11	chr12:57850715..57853202-chr12:57880450..57882915,3	K562	blood:
12	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:

No data

Variant related genes	Relation type
GLI1	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000258830	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000182199	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000175189	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11172142	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11172155	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs11830804	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs12227309	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs2943691	0.82[ASN][1000 genomes]
rs2943692	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2943693	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs507562	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538548	1.00[CEU][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs567895	1.00[CEU][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs7297282	0.81[EUR][1000 genomes]
rs7302906	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs9738646	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs473465	SP7	cis	parietal	SCAN
rs473465	DNAJC14	cis	cerebellum	SCAN
rs473465	KIAA0748	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57846800-57852200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:57846800-57852200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:57846800-57852600	Weak transcription	Fetal Lung	lung
4	chr12:57846800-57852600	Weak transcription	Left Ventricle	heart
5	chr12:57846800-57852600	Weak transcription	Right Atrium	heart
6	chr12:57846800-57852600	Weak transcription	NHDF-Ad	bronchial
7	chr12:57847800-57852600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:57848400-57852200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:57848600-57851200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr12:57848800-57852200	Weak transcription	Dnd41	blood
11	chr12:57848800-57852600	Active TSS	Liver	Liver
12	chr12:57849200-57852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:57849400-57851600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:57849400-57851600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:57849400-57852600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:57849600-57851400	Weak transcription	NHLF	lung
17	chr12:57849600-57852800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:57849800-57852400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:57849800-57852600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:57850000-57851600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:57850000-57851800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:57850000-57852200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:57850000-57852200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:57850000-57852200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:57850000-57852200	Enhancers	NHEK	skin
26	chr12:57850000-57852400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:57850000-57852400	Weak transcription	Colonic Mucosa	Colon
28	chr12:57850000-57852400	Enhancers	A549	lung
29	chr12:57850000-57852400	Enhancers	Hela-S3	cervix
30	chr12:57850000-57852600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:57850000-57852600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:57850000-57852600	Weak transcription	Fetal Kidney	kidney
33	chr12:57850200-57852000	Weak transcription	Primary B cells from cord blood	blood
34	chr12:57850200-57852000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:57850200-57852200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:57850200-57852200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:57850200-57852400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:57850200-57852400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:57850200-57852400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:57850200-57852600	Weak transcription	Thymus	Thymus
41	chr12:57850400-57851600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:57850400-57852000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:57850400-57852200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:57850400-57852200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:57850400-57852200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:57850400-57852200	Weak transcription	GM12878-XiMat	blood
47	chr12:57850400-57852400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:57850400-57852400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:57850400-57852400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:57850400-57852400	Weak transcription	Duodenum Mucosa	Duodenum

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