Variant report

Variant	rs752004
Chromosome Location	chr15:74329021-74329022
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	POLR2A	chr15:74329002-74329229	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:74328855-74329299	GM12878	blood:	n/a	n/a
3	CTCF	chr15:74328880-74329798	SK-N-SH	brain:	n/a	chr15:74329390-74329408
4	POLR2A	chr15:74328580-74329618	GM12878	blood:	n/a	n/a
5	CTCF	chr15:74328900-74329050	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:74328364-74329530	GM19193	blood:	n/a	n/a
7	POLR2A	chr15:74328239-74329208	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:74327911-74330065	K562	blood:	n/a	n/a
9	SMC3	chr15:74328963-74329697	SK-N-SH	brain:	n/a	chr15:74329392-74329406 chr15:74329392-74329402
10	RAD21	chr15:74329005-74329764	SK-N-SH	brain:	n/a	chr15:74329388-74329407 chr15:74329391-74329404 chr15:74329392-74329402 chr15:74329390-74329402
11	POLR2A	chr15:74328907-74329690	U87	brain:	n/a	n/a
12	POLR2A	chr15:74328943-74329311	GM12891	blood:	n/a	n/a
13	POLR2A	chr15:74328925-74329777	HL-60	blood:	n/a	n/a
14	CTCF	chr15:74328900-74329050	HRE	kidney:	n/a	n/a
15	POLR2A	chr15:74328992-74329515	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74243215..74244120-chr15:74328879..74329879,2	MCF-7	breast:
2	chr15:74218748..74221720-chr15:74327759..74329413,2	MCF-7	breast:
3	chr15:74264988..74266186-chr15:74328671..74329935,19	MCF-7	breast:
4	chr15:74176824..74179799-chr15:74328543..74330066,2	MCF-7	breast:
5	chr15:74328869..74331984-chr15:74335288..74339582,4	MCF-7	breast:
6	chr15:74264224..74266446-chr15:74328782..74330811,3	MCF-7	breast:
7	chr15:74265011..74265899-chr15:74328914..74329841,6	MCF-7	breast:

Variant related genes	Relation type
PML	TF binding region
ENSG00000261801	Chromatin interaction
ENSG00000129038	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1052242	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs1052246	0.95[ASN][1000 genomes]
rs10851866	0.88[ASN][1000 genomes]
rs10851867	0.87[ASN][1000 genomes]
rs10851868	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10851869	0.93[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs11072458	0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11072461	0.87[ASN][1000 genomes]
rs11072462	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11072463	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MKK][hapmap];0.90[ASN][1000 genomes]
rs11633735	0.91[ASN][1000 genomes]
rs11635930	0.88[ASN][1000 genomes]
rs11636065	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs11636150	0.95[ASN][1000 genomes]
rs11854321	0.88[ASN][1000 genomes]
rs11857498	0.88[ASN][1000 genomes]
rs12442211	0.82[CHB][hapmap]
rs12593528	0.90[ASN][1000 genomes]
rs12902857	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs12902945	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12911807	0.90[ASN][1000 genomes]
rs12911984	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1550435	0.89[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs2165242	0.93[ASN][1000 genomes]
rs2277599	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304716	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3784561	0.88[ASN][1000 genomes]
rs3784562	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4287518	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4547288	0.85[ASN][1000 genomes]
rs4886820	0.86[ASN][1000 genomes]
rs4886844	0.80[MEX][hapmap]
rs4886845	0.95[ASN][1000 genomes]
rs4886846	0.92[ASN][1000 genomes]
rs56194867	0.88[ASN][1000 genomes]
rs7183908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs734854	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs743580	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8027447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8028557	0.88[ASN][1000 genomes]
rs8038991	0.87[ASN][1000 genomes]
rs8039404	0.83[ASN][1000 genomes]
rs876383	0.84[MEX][hapmap]
rs9479	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[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	nsv518316	chr15:74290993-74331083	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs752004	CYP11A1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74288200-74331000	Weak transcription	Fetal Heart	heart
2	chr15:74289800-74331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:74292000-74329200	Weak transcription	Fetal Brain Male	brain
4	chr15:74302400-74331000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:74303600-74331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:74306400-74330600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:74311000-74330400	Strong transcription	GM12878-XiMat	blood
8	chr15:74312800-74330600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:74313000-74338600	Strong transcription	Primary T cells from cord blood	blood
10	chr15:74313600-74330000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:74314200-74338200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:74314400-74330400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:74314600-74330200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:74314600-74330400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:74314600-74338000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:74314800-74330400	Strong transcription	NHEK	skin
17	chr15:74316000-74330600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:74316400-74340400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:74318400-74329400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:74318400-74331000	Weak transcription	Hela-S3	cervix
21	chr15:74318400-74331000	Weak transcription	K562	blood
22	chr15:74318400-74340200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:74318400-74340400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:74318800-74330800	Strong transcription	Osteobl	bone
25	chr15:74321200-74329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:74321400-74330000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:74322800-74336600	Strong transcription	Primary B cells from cord blood	blood
28	chr15:74323400-74332400	Strong transcription	Thymus	Thymus
29	chr15:74323600-74330600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:74323800-74329400	Strong transcription	Fetal Intestine Large	intestine
31	chr15:74323800-74329800	Strong transcription	HSMM	muscle
32	chr15:74323800-74330400	Strong transcription	Dnd41	blood
33	chr15:74323800-74330800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:74323800-74330800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:74324400-74329200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:74324400-74329200	Strong transcription	Fetal Thymus	thymus
37	chr15:74324400-74329800	Strong transcription	Ovary	ovary
38	chr15:74324400-74330000	Strong transcription	Colonic Mucosa	Colon
39	chr15:74324600-74330600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr15:74324800-74329600	Strong transcription	Aorta	Aorta
41	chr15:74324800-74330400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:74324800-74330600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:74325000-74329200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr15:74325000-74329200	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr15:74325000-74329600	Strong transcription	Fetal Brain Female	brain
46	chr15:74325000-74330400	Strong transcription	Gastric	stomach
47	chr15:74325000-74330400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:74325000-74330600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:74325200-74329800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:74325200-74330200	Strong transcription	Muscle Satellite Cultured Cells	--

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