Variant report

Variant	rs1057899
Chromosome Location	chr2:46809621-46809622
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	GATA3	chr2:46809448-46809775	SH-SY5Y	brain:	n/a	n/a
2	GATA2	chr2:46809479-46809696	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000250116	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060656	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11901678	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903907	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13404342	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13410076	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376406	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1456018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17035361	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1809087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2276554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs3213985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768723	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3768724	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377377	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57134465	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57955462	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58101879	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58342271	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59183773	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59823825	0.87[ASN][1000 genomes]
rs60211996	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60738814	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61252474	1.00[ASN][1000 genomes]
rs6544904	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544908	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6727471	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs68104662	0.93[ASN][1000 genomes]
rs72875696	0.87[ASN][1000 genomes]
rs7563577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589908	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7592446	0.94[ASN][1000 genomes]
rs962467	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9808496	0.87[ASN][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	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv961403	chr2:46808120-46810006	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1057899	PIGF	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
3	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
5	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:46796000-46812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:46796600-46822000	Weak transcription	Fetal Brain Male	brain
8	chr2:46796800-46838000	Weak transcription	Fetal Kidney	kidney
9	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:46797800-46814400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:46797800-46841000	Weak transcription	K562	blood
12	chr2:46798200-46838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:46801200-46815000	Weak transcription	Psoas Muscle	Psoas
14	chr2:46802400-46815000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:46802400-46842600	Weak transcription	NHEK	skin
16	chr2:46802800-46837000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:46803200-46810800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:46803400-46810600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:46803400-46811600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:46803400-46811800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:46803400-46811800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:46803400-46818800	Weak transcription	HepG2	liver
23	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:46803600-46811800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:46803600-46811800	Strong transcription	Osteobl	bone
26	chr2:46803800-46810600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:46803800-46811800	Strong transcription	Adipose Nuclei	Adipose
28	chr2:46804000-46810400	Weak transcription	HUVEC	blood vessel
29	chr2:46804200-46812200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:46804400-46811400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:46805600-46815600	Weak transcription	Fetal Lung	lung
32	chr2:46805600-46836400	Weak transcription	HSMM	muscle
33	chr2:46806000-46811000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:46806200-46810800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:46806600-46813600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:46806600-46818800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:46807200-46810400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:46807200-46816800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:46807400-46821200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:46807600-46810200	Weak transcription	GM12878-XiMat	blood
41	chr2:46807600-46812400	Weak transcription	Small Intestine	intestine
42	chr2:46807600-46821200	Weak transcription	Thymus	Thymus
43	chr2:46807600-46828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:46807600-46842400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:46807600-46842600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:46807800-46810400	Weak transcription	Primary B cells from cord blood	blood
47	chr2:46807800-46810400	Weak transcription	Lung	lung
48	chr2:46807800-46810800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:46807800-46811600	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:46807800-46811600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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