Variant report

Variant	rs13410076
Chromosome Location	chr2:46815961-46815962
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	POLR2A	chr2:46811567-46816814	GM12878	blood:	n/a	n/a
2	FOXA1	chr2:46815839-46816366	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46769235..46772209-chr2:46814826..46816628,2	K562	blood:

Variant related genes	Relation type
PIGF	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

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

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

rs_ID	r²[population]
rs1057899	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]
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];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11901678	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903907	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];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1376406	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];0.93[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];0.87[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];0.93[TSI][hapmap];0.82[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];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377377	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57134465	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57955462	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58101879	0.82[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	0.86[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	0.82[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];0.93[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];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6727471	0.82[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];0.93[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];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589908	0.82[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];0.87[ASN][1000 genomes]
rs7592446	0.94[ASN][1000 genomes]
rs962467	0.81[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	nsv521013	chr2:46812338-46817644	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13410076	PIGF	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:46796600-46822000	Weak transcription	Fetal Brain Male	brain
4	chr2:46796800-46838000	Weak transcription	Fetal Kidney	kidney
5	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:46797800-46841000	Weak transcription	K562	blood
7	chr2:46798200-46838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:46802400-46842600	Weak transcription	NHEK	skin
9	chr2:46802800-46837000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:46803400-46818800	Weak transcription	HepG2	liver
11	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:46805600-46836400	Weak transcription	HSMM	muscle
13	chr2:46806600-46818800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:46807200-46816800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:46807400-46821200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:46807600-46821200	Weak transcription	Thymus	Thymus
17	chr2:46807600-46828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:46807600-46842400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:46807600-46842600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:46807800-46816800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:46807800-46818000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:46807800-46819400	Weak transcription	Dnd41	blood
23	chr2:46807800-46821600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:46807800-46821600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:46807800-46824600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:46807800-46825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:46807800-46828400	Weak transcription	Brain Substantia Nigra	brain
28	chr2:46807800-46835200	Weak transcription	Fetal Intestine Large	intestine
29	chr2:46807800-46835200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:46807800-46835400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:46807800-46835400	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:46807800-46836400	Weak transcription	Primary T cells from cord blood	blood
33	chr2:46807800-46842400	Weak transcription	NHLF	lung
34	chr2:46807800-46842600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:46807800-46842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:46807800-46842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:46807800-46842800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:46807800-46842800	Weak transcription	HSMMtube	muscle
39	chr2:46807800-46843000	Weak transcription	Brain Germinal Matrix	brain
40	chr2:46807800-46843000	Weak transcription	Fetal Stomach	stomach
41	chr2:46807800-46843200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:46808000-46816000	Weak transcription	Liver	Liver
43	chr2:46808000-46817800	Weak transcription	A549	lung
44	chr2:46808000-46819400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:46808000-46824200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:46808000-46836000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:46808000-46836400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:46808000-46838000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:46808000-46842800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:46808200-46836800	Weak transcription	Primary T cells fromperipheralblood	blood

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