Variant report

Variant	rs12581619
Chromosome Location	chr12:67169985-67169986
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	chr12:67169597..67171791-chr2:190019336..190021927,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10506495	0.85[ASN][1000 genomes]
rs10506498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784582	0.86[ASN][1000 genomes]
rs10878500	0.85[ASN][1000 genomes]
rs11176408	0.86[ASN][1000 genomes]
rs12578682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580348	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582532	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383107	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1480018	0.85[ASN][1000 genomes]
rs17827198	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2127535	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2870913	0.85[AMR][1000 genomes]
rs4344575	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60791637	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316508	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv915982	chr12:67050863-67189954	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1047085	chr12:67052384-67199621	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1040203	chr12:67056831-67189837	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv541520	chr12:67056831-67189837	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1053250	chr12:67067995-67381411	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1050547	chr12:67122154-67314886	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv541521	chr12:67122154-67314886	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv559209	chr12:67155610-67176792	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12581619	PSMD1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67168800-67170000	Enhancers	Fetal Muscle Leg	muscle
2	chr12:67168800-67170200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:67168800-67170600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:67168800-67171200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:67168800-67172600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:67169000-67170400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:67169000-67170600	Enhancers	Fetal Brain Female	brain
8	chr12:67169000-67170800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:67169000-67175800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:67169200-67174400	Weak transcription	Fetal Kidney	kidney
11	chr12:67169400-67170200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr12:67169400-67171000	Enhancers	Primary T cells from cord blood	blood
13	chr12:67169600-67170000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:67169600-67170000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:67169600-67170000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:67169600-67170000	Enhancers	Adipose Nuclei	Adipose
17	chr12:67169600-67170000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:67169600-67170000	Enhancers	Placenta	Placenta
19	chr12:67169600-67170000	Enhancers	NHEK	skin
20	chr12:67169600-67170200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:67169600-67170400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:67169600-67171800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr12:67169800-67170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:67169800-67171000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:67169800-67171600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:67169800-67171800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:67169800-67172000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:67169800-67172400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:67169800-67185200	Weak transcription	Pancreas	Pancrea

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