Variant report

Variant	rs12907836
Chromosome Location	chr15:50170635-50170636
allele	C/T
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	CEBPB	chr15:50169792-50170748	IMR90	lung:	n/a	chr15:50170334-50170345 chr15:50170334-50170343 chr15:50170332-50170343 chr15:50170334-50170343 chr15:50170627-50170638 chr15:50170627-50170638 chr15:50170332-50170345 chr15:50170334-50170343 chr15:50170626-50170643 chr15:50170334-50170343 chr15:50170627-50170640

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50168979..50170922-chr15:50428589..50430451,2	MCF-7	breast:
2	chr15:49911713..49913388-chr15:50169231..50171069,2	MCF-7	breast:

Variant related genes	Relation type
ATP8B4	TF binding region
ENSG00000259188	TF binding region
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1059851	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1059852	0.95[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs11070723	0.81[EUR][1000 genomes]
rs11070733	0.88[EUR][1000 genomes]
rs11630021	0.91[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs11632077	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11632116	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11633343	0.95[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs11633465	0.87[EUR][1000 genomes]
rs11633470	0.87[EUR][1000 genomes]
rs11633571	0.84[MEX][hapmap]
rs11633714	0.95[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs11633744	0.95[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs11633759	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs11634914	0.85[EUR][1000 genomes]
rs11636769	0.85[EUR][1000 genomes]
rs11639332	0.80[EUR][1000 genomes]
rs12148168	0.81[EUR][1000 genomes]
rs12901108	0.83[EUR][1000 genomes]
rs12903153	0.85[EUR][1000 genomes]
rs12909447	0.87[EUR][1000 genomes]
rs12915207	0.85[MEX][hapmap]
rs13329598	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16962994	0.85[MEX][hapmap]
rs16962999	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs17486097	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17486425	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs17486446	0.95[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs17486544	0.85[EUR][1000 genomes]
rs34404202	0.85[EUR][1000 genomes]
rs34449112	0.85[EUR][1000 genomes]
rs34561282	0.81[EUR][1000 genomes]
rs34751824	0.81[EUR][1000 genomes]
rs34845057	0.92[EUR][1000 genomes]
rs35827271	0.85[EUR][1000 genomes]
rs35899336	0.81[EUR][1000 genomes]
rs35958858	0.81[EUR][1000 genomes]
rs4275793	0.84[EUR][1000 genomes]
rs4347574	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4494482	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4494483	0.95[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4544192	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs61618346	0.92[EUR][1000 genomes]
rs6493383	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs66809683	0.90[EUR][1000 genomes]
rs71469605	0.83[EUR][1000 genomes]
rs7170482	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs7172553	0.85[EUR][1000 genomes]
rs7172585	0.85[EUR][1000 genomes]
rs72733056	0.85[EUR][1000 genomes]
rs8023895	0.85[EUR][1000 genomes]
rs8025533	0.95[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs8031452	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs8036570	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs8038434	0.86[CEU][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs8041979	0.91[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8042458	0.91[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12907836	CATSPER2P1	cis	cerebellum	SCAN
rs12907836	CTDSPL2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:50135800-50187400	Weak transcription	Liver	Liver
3	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:50161600-50175600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:50161800-50179000	Strong transcription	Primary hematopoietic stem cells	blood
8	chr15:50161800-50210600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:50162400-50172200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:50163000-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:50166000-50170800	Weak transcription	Left Ventricle	heart
12	chr15:50166600-50173000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:50167000-50171600	Enhancers	Colon Smooth Muscle	Colon
14	chr15:50167200-50171200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:50167600-50200800	Weak transcription	Spleen	Spleen
16	chr15:50168200-50171800	Enhancers	Rectal Smooth Muscle	rectum
17	chr15:50168400-50170800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:50168400-50171200	Enhancers	Fetal Muscle Leg	muscle
19	chr15:50168400-50171400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:50168400-50171400	Enhancers	NHDF-Ad	bronchial
21	chr15:50168400-50172600	Enhancers	Fetal Stomach	stomach
22	chr15:50168600-50171200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:50168600-50171200	Enhancers	Fetal Kidney	kidney
24	chr15:50168600-50171200	Enhancers	Right Atrium	heart
25	chr15:50168600-50171200	Enhancers	Osteobl	bone
26	chr15:50168800-50171000	Enhancers	Adipose Nuclei	Adipose
27	chr15:50169200-50171200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:50169200-50171200	Enhancers	NHLF	lung
29	chr15:50169400-50171000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:50169600-50170800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:50169600-50170800	Weak transcription	Small Intestine	intestine
32	chr15:50169600-50174400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:50169800-50170800	Weak transcription	Fetal Thymus	thymus
34	chr15:50169800-50170800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:50169800-50170800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:50169800-50175600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:50170000-50175800	Weak transcription	Aorta	Aorta
38	chr15:50170200-50171200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:50170200-50172000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:50170600-50171200	Enhancers	Placenta	Placenta
41	chr15:50170600-50171400	Enhancers	Fetal Lung	lung
42	chr15:50170600-50171600	Enhancers	Ovary	ovary
43	chr15:50170600-50175600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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