Variant report

Variant	rs12439819
Chromosome Location	chr15:99677707-99677708
allele	A/G
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:3)
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	POLR2A	chr15:99677192-99677709	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr15:99677060-99678008	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr15:99676989-99677742	Hela-S3	cervix:	n/a	n/a
4	EP300	chr15:99677260-99677832	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr15:99677005-99677916	Hela-S3	cervix:	n/a	n/a
6	MAX	chr15:99677140-99677921	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr15:99677142-99678000	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr15:99677108-99677947	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr15:99677005-99677991	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr15:99677040-99677936	ECC-1	luminal epithelium:	n/a	n/a
11	USF1	chr15:99677362-99677820	ECC-1	luminal epithelium:	n/a	n/a
12	USF1	chr15:99677315-99677809	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr15:99677425-99677785	A549	lung:	n/a	n/a
14	NFIC	chr15:99677139-99677936	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:99672945..99675578-chr15:99675648..99678258,3	K562	blood:
2	chr15:99676254..99679133-chr15:99680530..99682428,2	K562	blood:
3	chr15:99677279..99681777-chr15:99693510..99696751,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261616	TF binding region
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11247070	0.81[TSI][hapmap]
rs11247071	0.83[CHB][hapmap]
rs11247076	0.82[CHB][hapmap]
rs11247077	0.83[CHB][hapmap]
rs11247078	0.83[CHB][hapmap]
rs12439693	0.89[CHB][hapmap]
rs12439820	0.83[CHB][hapmap];0.81[TSI][hapmap]
rs12440477	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs12440640	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes]
rs12440982	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs12441965	0.83[CHB][hapmap];0.81[TSI][hapmap]
rs12441996	0.83[CHB][hapmap];0.81[TSI][hapmap]
rs12442235	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap]
rs12593076	0.83[CHB][hapmap];0.81[TSI][hapmap]
rs12594250	0.83[CHB][hapmap]
rs12594607	0.83[CHB][hapmap]
rs12595099	0.83[CHB][hapmap]
rs12901547	0.83[CHB][hapmap]
rs12902590	0.83[CHB][hapmap]
rs12906323	0.88[CHB][hapmap]
rs12906924	0.83[CHB][hapmap]
rs12907938	0.83[CHB][hapmap]
rs12914665	0.83[CHB][hapmap];0.81[TSI][hapmap]
rs1612365	0.94[CHB][hapmap]
rs1670229	0.94[CHB][hapmap]
rs1876741	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2006670	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2048303	0.83[CHB][hapmap]
rs2089708	0.83[CHB][hapmap]
rs2290352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2861371	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3134586	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3743242	0.94[EUR][1000 genomes]
rs3759903	0.83[CHB][hapmap];0.81[TSI][hapmap]
rs3961782	0.83[CHB][hapmap]
rs4965215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4965216	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4965446	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs4965448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4965451	0.91[CEU][hapmap];0.94[CHB][hapmap];0.80[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs58319155	0.94[AFR][1000 genomes]
rs58653169	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60513984	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163435	0.83[CHB][hapmap]
rs7169355	0.83[CHB][hapmap]
rs7170952	0.83[CHB][hapmap]
rs7178606	0.83[CHB][hapmap]
rs73480175	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73480191	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS 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	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS 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	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription 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	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12439819	SYNM	cis	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain
4	chr15:99664600-99678800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:99665000-99714200	Weak transcription	NHEK	skin
10	chr15:99665200-99679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:99666000-99683000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:99666200-99680400	Weak transcription	Fetal Brain Female	brain
14	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
15	chr15:99666400-99679800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:99667600-99679200	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:99669000-99679400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:99670800-99680600	Weak transcription	Thymus	Thymus
19	chr15:99671800-99679200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:99673000-99679400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
22	chr15:99673400-99679800	Genic enhancers	Stomach Smooth Muscle	stomach
23	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
24	chr15:99674600-99679800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr15:99676000-99678200	Strong transcription	Brain Anterior Caudate	brain
26	chr15:99676000-99678600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:99676000-99679000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:99676000-99679800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:99676000-99679800	Strong transcription	Fetal Intestine Large	intestine
30	chr15:99676000-99683200	Weak transcription	Stomach Mucosa	stomach
31	chr15:99676200-99677800	Strong transcription	Brain Hippocampus Middle	brain
32	chr15:99676200-99679000	Strong transcription	Left Ventricle	heart
33	chr15:99676200-99679800	Strong transcription	A549	lung
34	chr15:99676200-99682600	Weak transcription	NHDF-Ad	bronchial
35	chr15:99676200-99688800	Weak transcription	Brain Angular Gyrus	brain
36	chr15:99676200-99689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:99676200-99696200	Weak transcription	NH-A	brain
39	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
40	chr15:99676400-99678400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:99676400-99680400	Strong transcription	Fetal Stomach	stomach
42	chr15:99676400-99688600	Weak transcription	Fetal Heart	heart
43	chr15:99676400-99690200	Weak transcription	HSMM	muscle
44	chr15:99676600-99678000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:99676600-99678000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:99676600-99678000	Strong transcription	Fetal Lung	lung
47	chr15:99676600-99678400	Strong transcription	Right Ventricle	heart
48	chr15:99676600-99678800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:99676600-99679400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:99676600-99679600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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