Variant report

Variant	rs2458247
Chromosome Location	chr15:77281410-77281411
allele	C/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	WRNIP1	chr15:77280331-77281610	GM12878	blood:	n/a	n/a
2	IKZF1	chr15:77280398-77281704	GM12878	blood:	n/a	n/a
3	EBF1	chr15:77280229-77281792	GM12878	blood:	n/a	chr15:77280980-77280991 chr15:77280981-77280990
4	NFATC1	chr15:77280511-77281411	GM12878	blood:	n/a	n/a
5	SPI1	chr15:77280619-77281596	GM12878	blood:	n/a	chr15:77281138-77281151
6	POLR2A	chr15:77280560-77281750	GM12892	blood:	n/a	n/a
7	MAX	chr15:77280759-77281774	NB4	blood:	n/a	n/a
8	POLR2A	chr15:77280580-77281655	HL-60	blood:	n/a	n/a
9	MYC	chr15:77280766-77281811	NB4	blood:	n/a	n/a
10	SPI1	chr15:77280800-77281620	HL-60	blood:	n/a	chr15:77281138-77281151
11	MTA3	chr15:77280594-77281484	GM12878	blood:	n/a	n/a
12	RUNX3	chr15:77280451-77281545	GM12878	blood:	n/a	n/a
13	RELA	chr15:77280617-77281539	GM19099	blood:	n/a	n/a
14	POLR2A	chr15:77280836-77281458	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr15:77280525-77281895	GM12892	blood:	n/a	n/a
16	CHD2	chr15:77280669-77281714	GM12878	blood:	n/a	n/a
17	MTA3	chr15:77280056-77282118	GM12878	blood:	n/a	n/a
18	RELA	chr15:77280680-77281676	GM18951	blood:	n/a	n/a
19	IRF4	chr15:77280623-77281507	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:77280627-77281503	GM12892	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: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17380886	0.83[EUR][1000 genomes]
rs2221867	0.80[EUR][1000 genomes]
rs2458245	0.88[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2458250	0.87[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap]
rs2469229	0.81[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34370173	0.83[EUR][1000 genomes]
rs35018118	0.83[EUR][1000 genomes]
rs4886508	0.82[TSI][hapmap]
rs869884	0.89[TSI][hapmap];0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2458247	CRABP1	cis	parietal	SCAN
rs2458247	NEO1	cis	cerebellum	SCAN
rs2458247	ZNF291	cis	multi-tissue	Pritchard
rs2458247	PSTPIP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77274000-77287200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:77276200-77281600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:77278600-77282000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:77279000-77281600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:77279000-77281600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:77279000-77281800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr15:77279000-77281800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr15:77279000-77282000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr15:77279200-77281600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:77279200-77281600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr15:77279200-77281800	Enhancers	Primary B cells from cord blood	blood
12	chr15:77279200-77282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:77280000-77281600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:77280000-77281800	Enhancers	Primary B cells from peripheral blood	blood
15	chr15:77280000-77281800	Enhancers	Fetal Thymus	thymus
16	chr15:77280000-77281800	Enhancers	Left Ventricle	heart
17	chr15:77280000-77281800	Flanking Active TSS	GM12878-XiMat	blood
18	chr15:77280000-77282000	Enhancers	Fetal Muscle Leg	muscle
19	chr15:77280200-77281600	Enhancers	Primary hematopoietic stem cells	blood
20	chr15:77280200-77281600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:77280200-77282000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr15:77280200-77282000	Enhancers	Placenta	Placenta
23	chr15:77280200-77282000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr15:77280400-77281600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr15:77280400-77281600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr15:77280400-77281800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:77280400-77281800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:77280600-77281600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr15:77280600-77281600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr15:77280600-77281600	Enhancers	Fetal Intestine Small	intestine
31	chr15:77280600-77281600	Enhancers	Lung	lung
32	chr15:77280600-77281800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:77280600-77281800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:77280600-77281800	Enhancers	Liver	Liver
35	chr15:77280600-77281800	Enhancers	Right Atrium	heart
36	chr15:77280600-77282000	Enhancers	Fetal Muscle Trunk	muscle
37	chr15:77280800-77281600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:77280800-77281600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:77280800-77281600	Enhancers	Primary T cells from cord blood	blood
40	chr15:77280800-77281600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr15:77280800-77281800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr15:77280800-77281800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr15:77280800-77281800	Enhancers	Brain Anterior Caudate	brain
44	chr15:77280800-77281800	Enhancers	Fetal Stomach	stomach
45	chr15:77280800-77282000	Enhancers	Right Ventricle	heart
46	chr15:77280800-77282000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr15:77280800-77282200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr15:77281000-77281600	Enhancers	Thymus	Thymus
49	chr15:77281000-77281800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr15:77281000-77281800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links