Variant report

Variant	rs4993000
Chromosome Location	chr15:74282343-74282344
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	POLR2A	chr15:74282312-74282529	K562	blood:	n/a	n/a
2	JUND	chr15:74280035-74282439	SK-N-SH	brain:	n/a	chr15:74280603-74280614 chr15:74281363-74281374 chr15:74281361-74281371 chr15:74281910-74281917 chr15:74281360-74281372 chr15:74280607-74280615 chr15:74281361-74281371 chr15:74281910-74281919 chr15:74281361-74281371 chr15:74280605-74280617 chr15:74281361-74281371 chr15:74281910-74281918 chr15:74281361-74281370

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74281335..74284539-chr15:74284801..74290369,7	MCF-7	breast:
2	chr15:74272863..74275185-chr15:74282100..74283789,2	K562	blood:

Variant related genes	Relation type
PML	TF binding region
STOML1	TF binding region
ENSG00000140464	Chromatin interaction
ENSG00000067221	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10851869	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11072460	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636934	0.99[ASN][1000 genomes]
rs12101466	0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12102015	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12904518	0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs12909197	0.93[ASN][1000 genomes]
rs1550435	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2415188	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2507	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3816197	1.00[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs3816198	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886820	0.84[AFR][1000 genomes]
rs7171694	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7174985	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039184	0.98[ASN][1000 genomes]
rs9630436	0.83[AMR][1000 genomes];0.86[EUR][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	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4993000	PML	cis	parietal	SCAN
rs4993000	CYP11A1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74272600-74283800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:74273800-74283600	Enhancers	HMEC	breast
3	chr15:74273800-74283600	Enhancers	NHDF-Ad	bronchial
4	chr15:74273800-74283800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:74274600-74284000	Weak transcription	Ovary	ovary
6	chr15:74274800-74283800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:74275000-74283600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:74275000-74284000	Weak transcription	Aorta	Aorta
9	chr15:74275800-74282800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:74276000-74282800	Weak transcription	Fetal Brain Male	brain
11	chr15:74276000-74283400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:74276200-74282800	Genic enhancers	Fetal Muscle Leg	muscle
13	chr15:74276200-74283000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:74276600-74282800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:74276600-74283000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:74277200-74282800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:74277600-74283000	Weak transcription	Fetal Lung	lung
18	chr15:74277600-74283400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:74277800-74283400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr15:74277800-74283600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:74277800-74283600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:74278000-74283400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr15:74278400-74283000	Weak transcription	Fetal Heart	heart
24	chr15:74278400-74283000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:74278600-74283000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:74278600-74283600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:74279200-74283000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:74279200-74283400	Enhancers	HUVEC	blood vessel
29	chr15:74279400-74282600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:74279400-74283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:74279600-74283200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:74279600-74283800	Enhancers	NH-A	brain
33	chr15:74279800-74282400	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:74279800-74282800	Enhancers	Adipose Nuclei	Adipose
35	chr15:74279800-74283800	Enhancers	Stomach Mucosa	stomach
36	chr15:74280000-74282400	Enhancers	A549	lung
37	chr15:74280000-74283000	Weak transcription	Liver	Liver
38	chr15:74280200-74283600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:74280200-74283800	Enhancers	Esophagus	oesophagus
40	chr15:74280200-74284000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr15:74280400-74282600	Enhancers	GM12878-XiMat	blood
42	chr15:74280400-74282800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:74280400-74282800	Genic enhancers	Left Ventricle	heart
44	chr15:74280400-74283000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:74280600-74282800	Weak transcription	Fetal Intestine Large	intestine
46	chr15:74280600-74283400	Enhancers	Right Atrium	heart
47	chr15:74280800-74283000	Strong transcription	Thymus	Thymus
48	chr15:74280800-74283600	Enhancers	Colonic Mucosa	Colon
49	chr15:74280800-74284200	Enhancers	Small Intestine	intestine
50	chr15:74281000-74283000	Enhancers	NHLF	lung

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