Variant report

Variant	rs12309338
Chromosome Location	chr12:12421059-12421060
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:12419162-12421115	ECC-1	luminal epithelium:	n/a	chr12:12419896-12419906
2	TBP	chr12:12419334-12421120	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr12:12419564-12421375	A549	lung:	n/a	chr12:12419896-12419906
4	NRF1	chr12:12419545-12421108	SK-N-SH	brain:	n/a	chr12:12419957-12419968
5	MAX	chr12:12418483-12421114	A549	lung:	n/a	chr12:12419896-12419906
6	TCF12	chr12:12419443-12421132	ECC-1	luminal epithelium:	n/a	chr12:12420327-12420337
7	MXI1	chr12:12420816-12421162	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3AK20	chr12:12419520-12421129	MCF-7	breast:	n/a	n/a
9	GTF2F1	chr12:12421012-12421140	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr12:12419317-12421084	ECC-1	luminal epithelium:	n/a	n/a
11	REST	chr12:12418730-12421197	H1-neurons	neurons:	n/a	chr12:12419927-12419940 chr12:12419365-12419375 chr12:12420324-12420337 chr12:12419955-12419968
12	POLR2A	chr12:12419610-12421116	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr12:12419461-12421116	ECC-1	luminal epithelium:	n/a	chr12:12419896-12419906
14	SIN3A	chr12:12418526-12421272	H1-hESC	embryonic stem cell:	n/a	chr12:12419927-12419940 chr12:12419955-12419968

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:12419582..12421306-chr12:12876017..12878198,2	MCF-7	breast:
2	chr12:12378227..12379810-chr12:12418939..12421766,2	K562	blood:
3	chr12:12419134..12421122-chr12:12441823..12443690,2	MCF-7	breast:
4	chr12:12400936..12406172-chr12:12417674..12422348,4	K562	blood:
5	chr12:12229163..12231212-chr12:12420011..12422255,2	K562	blood:
6	chr12:12390182..12397827-chr12:12417123..12421502,7	MCF-7	breast:
7	chr12:12419370..12422118-chr12:12510348..12512093,2	MCF-7	breast:
8	chr12:12393044..12397840-chr12:12419223..12421821,5	MCF-7	breast:
9	chr12:12230786..12232660-chr12:12419937..12421467,2	K562	blood:
10	chr12:12419774..12421330-chr12:12508637..12511348,2	MCF-7	breast:
11	chr12:12420270..12422598-chr12:12424124..12428048,6	K562	blood:
12	chr12:12411626..12414518-chr12:12420226..12422396,2	K562	blood:
13	chr12:12401851..12404835-chr12:12418306..12421349,3	MCF-7	breast:
14	chr12:12420321..12422188-chr12:12434856..12437059,2	MCF-7	breast:
15	chr12:12420258..12422244-chr12:12868437..12870930,2	K562	blood:
16	chr12:12418062..12421378-chr12:12712958..12715949,4	MCF-7	breast:
17	chr12:12418888..12421558-chr12:12875681..12878464,3	MCF-7	breast:
18	chr12:12223594..12226384-chr12:12419195..12421286,2	MCF-7	breast:

No data

Variant related genes	Relation type
LRP6	TF binding region
ENSG00000111276	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000270857	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000256658	Chromatin interaction
ENSG00000070018	Chromatin interaction
ENSG00000207010	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000199551	Chromatin interaction
ENSG00000121380	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10082834	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10083170	0.81[AMR][1000 genomes]
rs10466847	1.00[ASN][1000 genomes]
rs10466848	1.00[ASN][1000 genomes]
rs10845497	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054695	1.00[ASN][1000 genomes]
rs11054696	1.00[ASN][1000 genomes]
rs11054702	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054705	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054706	1.00[ASN][1000 genomes]
rs11054707	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054709	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054710	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054713	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054732	1.00[JPT][hapmap]
rs11054746	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054767	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1123213	1.00[ASN][1000 genomes]
rs11829211	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11831610	1.00[ASN][1000 genomes]
rs12296239	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12305378	1.00[ASN][1000 genomes]
rs12306293	1.00[ASN][1000 genomes]
rs12306537	1.00[ASN][1000 genomes]
rs12307111	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12309246	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12310020	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12311202	1.00[ASN][1000 genomes]
rs12311922	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12316043	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12422890	1.00[ASN][1000 genomes]
rs12424332	1.00[ASN][1000 genomes]
rs12424361	1.00[ASN][1000 genomes]
rs12425185	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12425699	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13377971	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907789	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907821	1.00[YRI][hapmap]
rs28448423	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56259928	1.00[ASN][1000 genomes]
rs58682800	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59386755	1.00[ASN][1000 genomes]
rs7308022	1.00[JPT][hapmap]
rs7311064	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	1.00[JPT][hapmap]
rs7979919	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9630249	1.00[ASN][1000 genomes]
rs9630250	1.00[ASN][1000 genomes]
rs9630266	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12309338	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12418000-12421200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:12418400-12421200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr12:12420400-12421200	Flanking Active TSS	Hela-S3	cervix
4	chr12:12420600-12421200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
5	chr12:12420600-12421200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:12420600-12421200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:12420600-12421200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr12:12420600-12421200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:12420600-12421200	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr12:12420600-12421200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr12:12420600-12421200	Flanking Active TSS	A549	lung
12	chr12:12420600-12421200	Flanking Active TSS	NHEK	skin
13	chr12:12420600-12421400	Enhancers	Pancreas	Pancrea
14	chr12:12420800-12421200	Flanking Active TSS	Fetal Brain Male	brain
15	chr12:12420800-12421200	Enhancers	Fetal Lung	lung
16	chr12:12420800-12421200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr12:12420800-12421400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:12420800-12425600	Weak transcription	HSMM	muscle
19	chr12:12421000-12421200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:12421000-12421200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:12421000-12421200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:12421000-12421200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:12421000-12421200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr12:12421000-12421200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:12421000-12421200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:12421000-12421200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:12421000-12421200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:12421000-12421200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:12421000-12421200	Enhancers	Liver	Liver
30	chr12:12421000-12421200	Enhancers	Colon Smooth Muscle	Colon
31	chr12:12421000-12421200	Flanking Active TSS	Fetal Brain Female	brain
32	chr12:12421000-12421200	Enhancers	Fetal Intestine Large	intestine
33	chr12:12421000-12421200	Enhancers	Fetal Intestine Small	intestine
34	chr12:12421000-12421200	Active TSS	Fetal Kidney	kidney
35	chr12:12421000-12421200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:12421000-12421200	Active TSS	GM12878-XiMat	blood
37	chr12:12421000-12421200	Enhancers	HMEC	breast
38	chr12:12421000-12421200	Enhancers	HUVEC	blood vessel
39	chr12:12421000-12421400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:12421000-12421400	Enhancers	HepG2	liver
41	chr12:12421000-12421800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:12421000-12422200	Weak transcription	Placenta	Placenta
43	chr12:12421000-12423800	Weak transcription	Right Atrium	heart
44	chr12:12421000-12425200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:12421000-12425200	Weak transcription	NHDF-Ad	bronchial
46	chr12:12421000-12425200	Weak transcription	Osteobl	bone
47	chr12:12421000-12425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:12421000-12425600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:12421000-12425600	Weak transcription	NHLF	lung
50	chr12:12421000-12425800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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