Variant report

Variant	rs12592370
Chromosome Location	chr15:74311689-74311690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74311100..74312963-chr15:74315126..74316880,2	MCF-7	breast:
2	chr15:74310869..74312553-chr15:74315639..74317174,2	MCF-7	breast:
3	chr15:74301606..74304928-chr15:74311289..74313632,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140464	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10162627	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1052242	1.00[CEU][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1052246	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10851868	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072458	0.81[CEU][hapmap]
rs11072463	0.83[MEX][hapmap]
rs11072464	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072465	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072467	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072469	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11633520	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11633735	0.81[AMR][1000 genomes]
rs11636016	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11636065	1.00[CEU][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636150	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12593528	0.86[AMR][1000 genomes]
rs12901603	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902857	1.00[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12904213	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908748	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911984	0.81[AMR][1000 genomes]
rs12912395	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12917179	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550434	0.81[YRI][hapmap]
rs2165242	0.81[AMR][1000 genomes]
rs2277599	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2304715	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304716	0.96[MEX][hapmap]
rs2304717	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304718	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784561	0.82[AMR][1000 genomes]
rs3784562	0.96[CEU][hapmap]
rs4287518	0.81[AMR][1000 genomes]
rs4886820	0.81[AMR][1000 genomes]
rs4886844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886845	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886846	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs734854	0.83[MEX][hapmap]
rs743581	0.82[ASN][1000 genomes]
rs8027327	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8027447	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8027774	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8028557	0.85[AMR][1000 genomes]
rs8039276	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8043489	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12592370	CYP11A1	cis	cerebellum	SCAN
rs12592370	PML	cis	multi-tissue	Pritchard
rs12592370	ADPGK	cis	parietal	SCAN
rs12592370	LARP6	cis	parietal	SCAN
rs12592370	BBS4	cis	parietal	SCAN
rs12592370	STOML1	cis	cerebellum	SCAN
rs12592370	STOML1	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr15:74290000-74314800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:74291000-74314800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:74291000-74315000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:74291000-74315200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:74291800-74314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:74292000-74315200	Weak transcription	Fetal Brain Female	brain
9	chr15:74292000-74329200	Weak transcription	Fetal Brain Male	brain
10	chr15:74296600-74315200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:74296800-74315200	Weak transcription	Brain Germinal Matrix	brain
12	chr15:74297000-74315200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:74297000-74315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:74299200-74315400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:74299400-74315400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:74300000-74314800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:74300400-74315800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:74300600-74315200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:74300800-74315200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr15:74300800-74315200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:74300800-74315200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:74300800-74326000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:74302400-74312800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:74302400-74331000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:74303600-74331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:74303800-74315000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:74304000-74314800	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:74304000-74314800	Weak transcription	NH-A	brain
29	chr15:74304000-74315200	Weak transcription	Brain Anterior Caudate	brain
30	chr15:74304000-74315200	Weak transcription	Brain Substantia Nigra	brain
31	chr15:74304000-74315200	Weak transcription	Psoas Muscle	Psoas
32	chr15:74304000-74326000	Weak transcription	Fetal Kidney	kidney
33	chr15:74304200-74314400	Weak transcription	Dnd41	blood
34	chr15:74304200-74314600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:74304200-74314800	Weak transcription	Ovary	ovary
36	chr15:74304200-74314800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:74304200-74315000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:74304200-74315000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:74304200-74315200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:74304200-74315200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:74304200-74315200	Weak transcription	Colonic Mucosa	Colon
42	chr15:74304200-74315200	Weak transcription	Fetal Lung	lung
43	chr15:74304200-74315200	Weak transcription	Gastric	stomach
44	chr15:74304200-74315200	Weak transcription	Pancreas	Pancrea
45	chr15:74304200-74315400	Weak transcription	Brain Angular Gyrus	brain
46	chr15:74304200-74316800	Weak transcription	Right Atrium	heart
47	chr15:74304400-74313000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:74304400-74315200	Weak transcription	Placenta	Placenta
49	chr15:74304400-74315800	Weak transcription	HepG2	liver
50	chr15:74304400-74316000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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