Variant report

Variant	rs2458246
Chromosome Location	chr15:77281858-77281859
allele	A/T
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	EBF1	chr15:77281468-77281859	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:77281776-77281885	MCF-7	breast:	n/a	n/a
3	POLR2A	chr15:77280525-77281895	GM12892	blood:	n/a	n/a
4	MTA3	chr15:77280056-77282118	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77280561..77283110-chr15:77283637..77286723,3	MCF-7	breast:
2	chr15:77280526..77282215-chr15:77292098..77294137,2	K562	blood:

Variant related genes	Relation type
PSTPIP1	TF binding region
ENSG00000140368	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1022198	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1567670	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1877435	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1877436	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2254441	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2458254	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2469200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469203	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2469227	1.00[ASN][1000 genomes]
rs2469232	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7175783	0.82[AMR][1000 genomes]
rs8030698	0.81[AMR][1000 genomes];0.81[EUR][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	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1808532	chr15:77257714-77332539	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1043017	chr15:77266776-77309938	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1035874	chr15:77266776-77328742	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2458246	PSTPIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77274000-77287200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:77278600-77282000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:77279000-77282000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr15:77279200-77282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:77280000-77282000	Enhancers	Fetal Muscle Leg	muscle
6	chr15:77280200-77282000	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr15:77280200-77282000	Enhancers	Placenta	Placenta
8	chr15:77280200-77282000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr15:77280600-77282000	Enhancers	Fetal Muscle Trunk	muscle
10	chr15:77280800-77282000	Enhancers	Right Ventricle	heart
11	chr15:77280800-77282000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:77280800-77282200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr15:77281200-77282000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:77281200-77282000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
15	chr15:77281200-77286400	Weak transcription	Colonic Mucosa	Colon
16	chr15:77281200-77286400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:77281400-77282000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:77281400-77285800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:77281400-77286000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:77281400-77286400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:77281600-77282000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:77281600-77282000	Enhancers	Adipose Nuclei	Adipose
23	chr15:77281600-77282000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr15:77281600-77284600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:77281600-77285600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:77281600-77285600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:77281600-77285600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:77281600-77285600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:77281600-77285600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:77281600-77285800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:77281600-77285800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr15:77281600-77286000	Weak transcription	Primary T cells from cord blood	blood
33	chr15:77281600-77286000	Weak transcription	Lung	lung
34	chr15:77281600-77286200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:77281600-77286400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:77281600-77287800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:77281600-77289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:77281800-77282000	Genic enhancers	Spleen	Spleen
39	chr15:77281800-77283000	Weak transcription	Pancreas	Pancrea
40	chr15:77281800-77283200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:77281800-77283200	Weak transcription	Primary B cells from cord blood	blood
42	chr15:77281800-77283200	Weak transcription	Right Atrium	heart
43	chr15:77281800-77283400	Enhancers	GM12878-XiMat	blood
44	chr15:77281800-77284800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:77281800-77284800	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:77281800-77285600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:77281800-77285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:77281800-77285800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:77281800-77286000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:77281800-77286400	Weak transcription	Fetal Thymus	thymus

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