Variant report

Variant	rs12912578
Chromosome Location	chr15:74473073-74473074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:74472737-74473243	GM12878	blood:	n/a	chr15:74473013-74473022 chr15:74473007-74473020 chr15:74473006-74473019 chr15:74473010-74473017
2	SPI1	chr15:74472812-74473156	GM12891	blood:	n/a	chr15:74473013-74473022 chr15:74473007-74473020 chr15:74473006-74473019 chr15:74473010-74473017
3	SPI1	chr15:74472824-74473095	GM12891	blood:	n/a	chr15:74473013-74473022 chr15:74473007-74473020 chr15:74473006-74473019 chr15:74473010-74473017
4	FOS	chr15:74472453-74473157	HUVEC	blood vessel:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
5	JUND	chr15:74469814-74473399	SK-N-SH	brain:	n/a	chr15:74472604-74472614 chr15:74472604-74472614 chr15:74470403-74470410
6	GATA2	chr15:74472637-74473235	HUVEC	blood vessel:	n/a	chr15:74473010-74473020 chr15:74472822-74472832
7	SPI1	chr15:74472898-74473105	GM12878	blood:	n/a	chr15:74473013-74473022 chr15:74473007-74473020 chr15:74473006-74473019 chr15:74473010-74473017
8	SPI1	chr15:74472861-74473168	GM12878	blood:	n/a	chr15:74473013-74473022 chr15:74473007-74473020 chr15:74473006-74473019 chr15:74473010-74473017
9	NFIC	chr15:74471540-74473134	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr15:74471467-74473216	SK-N-SH	brain:	n/a	chr15:74472614-74472623 chr15:74471501-74471508

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74471188..74474733-chr15:74480852..74485546,5	MCF-7	breast:
2	chr15:74471878..74474660-chr15:74491803..74495339,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261543	TF binding region
ENSG00000137868	Chromatin interaction
ENSG00000259264	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11630317	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11630924	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs11631509	0.86[EUR][1000 genomes]
rs11631944	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11639090	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11639369	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11854957	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11855667	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs11857410	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12899173	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12907503	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12911581	0.85[EUR][1000 genomes]
rs12912258	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12913041	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs13259	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2062309	0.97[EUR][1000 genomes]
rs2415169	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899824	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34147822	0.89[EUR][1000 genomes]
rs34573746	0.88[EUR][1000 genomes]
rs34868798	0.98[EUR][1000 genomes]
rs351242	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs35255788	0.89[EUR][1000 genomes]
rs35462746	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35661273	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3848160	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3848161	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3888004	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs409856	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	0.89[EUR][1000 genomes]
rs62003661	0.86[EUR][1000 genomes]
rs62005707	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62005709	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62005710	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62005711	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71399778	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs733163	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs8037531	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs923118	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes]
rs9630417	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.97[EUR][1000 genomes]
rs971755	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs971756	0.82[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs971757	0.82[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1050884	chr15:74394983-74489413	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12912578	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74464800-74473600	Enhancers	Right Ventricle	heart
2	chr15:74466200-74492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:74466600-74473200	Enhancers	HSMMtube	muscle
4	chr15:74466600-74480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:74467200-74473600	Enhancers	Right Atrium	heart
6	chr15:74467400-74473400	Genic enhancers	Fetal Stomach	stomach
7	chr15:74467400-74473800	Enhancers	NHDF-Ad	bronchial
8	chr15:74467600-74473200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:74467800-74473600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:74468400-74473400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr15:74468400-74473600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:74468600-74473200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:74468600-74473600	Enhancers	NH-A	brain
14	chr15:74469000-74473200	Enhancers	NHLF	lung
15	chr15:74469200-74473200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:74469200-74474000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:74469200-74491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:74469400-74487600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:74470000-74473400	Enhancers	HUVEC	blood vessel
21	chr15:74470000-74473800	Enhancers	Left Ventricle	heart
22	chr15:74470600-74473600	Enhancers	Ovary	ovary
23	chr15:74470600-74474000	Enhancers	Lung	lung
24	chr15:74470600-74475600	Weak transcription	Fetal Kidney	kidney
25	chr15:74470600-74484000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:74470800-74492800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:74471000-74473600	Enhancers	Fetal Muscle Leg	muscle
28	chr15:74471200-74473600	Enhancers	Fetal Thymus	thymus
29	chr15:74471200-74473600	Enhancers	HMEC	breast
30	chr15:74471200-74473800	Enhancers	Spleen	Spleen
31	chr15:74471400-74473200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:74471400-74473200	Enhancers	Fetal Lung	lung
33	chr15:74471400-74473400	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr15:74471400-74473800	Enhancers	Esophagus	oesophagus
35	chr15:74471400-74475200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:74471600-74473200	Enhancers	Brain Cingulate Gyrus	brain
37	chr15:74471800-74473400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:74471800-74473600	Enhancers	Fetal Brain Female	brain
39	chr15:74471800-74478000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:74472000-74477400	Genic enhancers	Placenta	Placenta
41	chr15:74472200-74473400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:74472200-74473600	Enhancers	Pancreas	Pancrea
43	chr15:74472200-74473600	Enhancers	GM12878-XiMat	blood
44	chr15:74472200-74474600	Strong transcription	Fetal Intestine Small	intestine
45	chr15:74472400-74473200	Weak transcription	Colonic Mucosa	Colon
46	chr15:74472400-74473400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:74472400-74473600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:74472400-74473800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:74472400-74473800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr15:74472400-74473800	Enhancers	Hela-S3	cervix

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