Variant report

Variant	rs2433325
Chromosome Location	chr4:95441592-95441593
allele	A/G
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	SPI1	chr4:95441567-95441922	GM12891	blood:	n/a	chr4:95441738-95441751
2	RCOR1	chr4:95441030-95441892	K562	blood:	n/a	n/a
3	STAT3	chr4:95441591-95441791	GM12878	blood:	n/a	n/a
4	SPI1	chr4:95441484-95441869	HL-60	blood:	n/a	chr4:95441738-95441751
5	BHLHE40	chr4:95441093-95441674	K562	blood:	n/a	n/a
6	FOXP2	chr4:95441250-95441625	SK-N-MC	brain:	n/a	n/a
7	TBP	chr4:95441313-95441787	GM12878	blood:	n/a	n/a
8	SPI1	chr4:95441391-95442020	HL-60	blood:	n/a	chr4:95441738-95441751
9	POLR2A	chr4:95441215-95441629	SK-N-MC	brain:	n/a	n/a
10	SPI1	chr4:95441279-95441972	GM12878	blood:	n/a	chr4:95441738-95441751
11	SPI1	chr4:95441554-95441872	GM12878	blood:	n/a	chr4:95441738-95441751
12	SPI1	chr4:95441577-95441968	GM12891	blood:	n/a	chr4:95441738-95441751
13	TEAD4	chr4:95441107-95441948	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:95440363..95442905-chr4:95447523..95451305,3	K562	blood:
2	chr4:95438774..95443250-chr4:95444770..95449023,5	K562	blood:
3	chr4:95381090..95383308-chr4:95441129..95442630,2	K562	blood:

Variant related genes	Relation type
PDLIM5	TF binding region
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1353044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433317	0.94[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433324	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2438142	0.94[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2438143	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452554	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs2452559	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452560	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452561	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2452562	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452564	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452565	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2452566	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2452568	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510778	0.94[CEU][hapmap]
rs2510785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510786	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510787	0.92[CEU][hapmap]
rs2510788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510791	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2510792	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2510794	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2510795	0.94[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2510802	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs2577056	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2433325	RAP1GDS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95430000-95456200	Weak transcription	Small Intestine	intestine
3	chr4:95430600-95444000	Weak transcription	HSMMtube	muscle
4	chr4:95435800-95444600	Enhancers	Fetal Heart	heart
5	chr4:95436200-95441600	Enhancers	Liver	Liver
6	chr4:95436400-95447200	Enhancers	Colon Smooth Muscle	Colon
7	chr4:95436800-95447800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:95437200-95448400	Weak transcription	HSMM	muscle
9	chr4:95437400-95445000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:95437600-95456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:95437800-95448600	Weak transcription	NHEK	skin
12	chr4:95438000-95448400	Weak transcription	Fetal Intestine Large	intestine
13	chr4:95438200-95442000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:95438200-95448800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:95438200-95454600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:95438400-95454800	Weak transcription	Hela-S3	cervix
17	chr4:95438600-95442600	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr4:95438600-95445000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:95438800-95443800	Weak transcription	NHLF	lung
20	chr4:95438800-95444400	Weak transcription	HMEC	breast
21	chr4:95438800-95446800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:95438800-95448600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:95439000-95447000	Weak transcription	HepG2	liver
24	chr4:95439200-95441600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr4:95439200-95442600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr4:95439400-95448800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:95439800-95441600	Enhancers	Placenta	Placenta
28	chr4:95439800-95444600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:95440000-95441600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:95440000-95441600	Enhancers	Primary B cells from peripheral blood	blood
31	chr4:95440000-95441600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr4:95440000-95441600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:95440000-95441600	Genic enhancers	Left Ventricle	heart
34	chr4:95440000-95441800	Flanking Active TSS	GM12878-XiMat	blood
35	chr4:95440000-95442200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:95440000-95442200	Enhancers	Primary B cells from cord blood	blood
37	chr4:95440200-95441600	Enhancers	Rectal Smooth Muscle	rectum
38	chr4:95440200-95441800	Enhancers	Brain Anterior Caudate	brain
39	chr4:95440200-95442000	Enhancers	Primary T cells from cord blood	blood
40	chr4:95440200-95442600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr4:95440400-95441800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:95440400-95441800	Enhancers	K562	blood
43	chr4:95440400-95443400	Genic enhancers	Osteobl	bone
44	chr4:95440400-95443800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:95440400-95444200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:95440400-95444800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:95440400-95446200	Weak transcription	Ovary	ovary
48	chr4:95440400-95447000	Weak transcription	Fetal Lung	lung
49	chr4:95440400-95448400	Weak transcription	Brain Substantia Nigra	brain
50	chr4:95440400-95455000	Weak transcription	H1 Cell Line	embryonic stem cell

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