Variant report

Variant	rs6772
Chromosome Location	chr15:74338939-74338940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74328869..74331984-chr15:74335288..74339582,4	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1036673	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886860	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886861	0.90[ASN][1000 genomes]
rs4886867	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7179827	0.90[ASN][1000 genomes]
rs7180506	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
5	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv457203	chr15:74308940-74347723	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv569971	chr15:74308940-74347723	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
9	nsv510666	chr15:74310738-74394745	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv817697	chr15:74336633-74343330	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6772	PML	cis	multi-tissue	Pritchard
rs6772	CYP11A1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74316400-74340400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:74318400-74340200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:74318400-74340400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:74326600-74340200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:74327800-74346000	Weak transcription	Psoas Muscle	Psoas
6	chr15:74328600-74346200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:74328800-74340000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:74329000-74344000	Weak transcription	Small Intestine	intestine
9	chr15:74329200-74339000	Weak transcription	Fetal Thymus	thymus
10	chr15:74329200-74340400	Weak transcription	Liver	Liver
11	chr15:74329200-74340600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:74329200-74343200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:74329400-74340200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:74329800-74340400	Weak transcription	Fetal Brain Male	brain
15	chr15:74329800-74340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:74330000-74340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:74330000-74340600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:74330000-74343000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:74330400-74340200	Weak transcription	Dnd41	blood
20	chr15:74330400-74340400	Weak transcription	GM12878-XiMat	blood
21	chr15:74330600-74340200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:74331600-74340400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:74331800-74339000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:74332600-74340400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:74333000-74343000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:74333200-74340200	Weak transcription	Fetal Lung	lung
27	chr15:74333200-74340400	Weak transcription	NHEK	skin
28	chr15:74333200-74342600	Weak transcription	HMEC	breast
29	chr15:74333400-74340400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:74333400-74340400	Weak transcription	Right Atrium	heart
31	chr15:74333400-74341000	Weak transcription	HUVEC	blood vessel
32	chr15:74333600-74339600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:74334000-74342600	Weak transcription	Pancreas	Pancrea
34	chr15:74334000-74346600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:74334200-74340200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:74334200-74342400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:74334400-74340400	Weak transcription	Fetal Kidney	kidney
38	chr15:74334800-74340400	Weak transcription	Stomach Mucosa	stomach
39	chr15:74335200-74340400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:74335400-74340400	Weak transcription	HSMM	muscle
41	chr15:74335600-74340400	Weak transcription	Osteobl	bone
42	chr15:74335800-74340400	Weak transcription	Brain Substantia Nigra	brain
43	chr15:74336000-74340400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:74336000-74340600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:74336000-74342600	Weak transcription	Fetal Intestine Large	intestine
46	chr15:74336200-74340200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:74336200-74346200	Weak transcription	Brain Angular Gyrus	brain
48	chr15:74336400-74339400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr15:74336400-74339800	Weak transcription	HSMMtube	muscle
50	chr15:74336600-74340600	Weak transcription	Primary B cells from cord blood	blood

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