Variant report

Variant	rs591874
Chromosome Location	chr12:121571465-121571466
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121569906..121572539-chr12:121647803..121649868,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10849844	0.85[CHB][hapmap]
rs11065434	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065442	0.99[ASN][1000 genomes]
rs11065450	0.91[MEX][hapmap]
rs1180011	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1180012	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1180015	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1183296	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1185268	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs169631	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs169632	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs169633	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1794897	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796412	0.94[TSI][hapmap]
rs1796421	0.94[TSI][hapmap]
rs1796422	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs183283	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs189989	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs208277	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs208280	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs208284	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208287	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs208290	0.85[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208293	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs208294	0.90[CHB][hapmap]
rs2263271	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393799	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686352	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs500930	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs501167	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs523977	0.83[AMR][1000 genomes]
rs570984	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575572	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582315	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636719	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656612	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs665794	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs671684	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs676262	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs685019	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309886	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs591874	PITPNM2	cis	parietal	SCAN
rs591874	ORAI1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121570200-121571600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:121570200-121571600	Enhancers	Small Intestine	intestine
3	chr12:121570200-121571800	Active TSS	Brain Hippocampus Middle	brain
4	chr12:121570200-121573000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:121570400-121571600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:121570400-121571600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr12:121570400-121571600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr12:121570400-121571600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr12:121570400-121571600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr12:121570400-121571600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr12:121570400-121571600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr12:121570400-121571600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:121570400-121571600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:121570400-121571600	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr12:121570400-121571600	Flanking Active TSS	Liver	Liver
16	chr12:121570400-121571600	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr12:121570400-121571600	Enhancers	Fetal Brain Male	brain
18	chr12:121570400-121571600	Flanking Active TSS	NHLF	lung
19	chr12:121570400-121571800	Flanking Active TSS	Dnd41	blood
20	chr12:121570400-121572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:121570400-121572600	Active TSS	Brain Angular Gyrus	brain
22	chr12:121570600-121571600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr12:121570600-121571600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr12:121570600-121571600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:121570600-121571600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr12:121570600-121571600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr12:121570600-121571600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr12:121570600-121571600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:121570600-121571600	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr12:121570600-121571600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:121570600-121571600	Flanking Active TSS	GM12878-XiMat	blood
32	chr12:121570600-121571600	Flanking Active TSS	NHEK	skin
33	chr12:121570600-121571800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr12:121570600-121571800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:121570600-121572600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr12:121570800-121571600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr12:121570800-121571600	Enhancers	A549	lung
38	chr12:121570800-121571800	Active TSS	Brain Cingulate Gyrus	brain
39	chr12:121570800-121573400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:121570800-121575000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:121571000-121571600	Enhancers	Fetal Heart	heart
42	chr12:121571000-121571800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:121571000-121571800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr12:121571200-121571600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:121571200-121571600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:121571200-121571600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr12:121571200-121571600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr12:121571200-121571600	Enhancers	HMEC	breast
49	chr12:121571200-121572000	Enhancers	Stomach Mucosa	stomach
50	chr12:121571200-121573000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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