Variant report

Variant	rs6809003
Chromosome Location	chr3:156861750-156861751
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156851307..156853070-chr3:156861254..156863346,2	MCF-7	breast:
2	chr3:156860100..156862214-chr3:156863800..156865338,3	MCF-7	breast:
3	chr3:156266499..156269259-chr3:156860290..156863068,2	K562	blood:
4	chr3:156829814..156832338-chr3:156860168..156861958,2	K562	blood:

Variant related genes	Relation type
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10212545	0.83[EUR][1000 genomes]
rs10451871	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10451916	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1046938	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[ASN][1000 genomes]
rs10513507	0.92[CEU][hapmap]
rs1060543	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11926167	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629549	0.86[EUR][1000 genomes]
rs12637518	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12696045	0.82[ASN][1000 genomes]
rs13061214	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs13081036	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs13081038	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13084070	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392799	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1403104	0.81[CEU][hapmap];0.95[TSI][hapmap]
rs1500925	0.82[ASN][1000 genomes]
rs1587534	0.82[EUR][1000 genomes]
rs1587535	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1608127	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs16827308	0.81[CEU][hapmap];0.93[YRI][hapmap]
rs16827322	0.81[CEU][hapmap];0.90[TSI][hapmap]
rs16827350	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2088814	0.85[EUR][1000 genomes]
rs2133952	0.86[EUR][1000 genomes]
rs28384296	0.80[EUR][1000 genomes]
rs35217153	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3749214	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs4368452	0.86[EUR][1000 genomes]
rs4383468	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4563363	0.87[EUR][1000 genomes]
rs4632503	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680344	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680346	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680347	0.83[CEU][hapmap]
rs4680348	0.82[EUR][1000 genomes]
rs6441114	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441121	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs6441122	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441123	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs67196056	0.83[EUR][1000 genomes]
rs6767619	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773061	0.82[ASN][1000 genomes]
rs6780831	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781991	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789178	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6805114	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808284	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6808457	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6809394	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620178	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625059	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs7636185	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638194	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7642179	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7647643	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs924517	0.85[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs9289978	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289979	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9811195	0.81[ASN][1000 genomes]
rs9827676	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9831830	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9838724	0.85[EUR][1000 genomes]
rs9848409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849168	0.81[ASN][1000 genomes]
rs9858423	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9861469	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9867618	0.85[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]

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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6809003	PTX3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848400-156866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:156848400-156866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156849000-156861800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:156849000-156862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:156849800-156864000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:156853200-156865400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:156853400-156872000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:156855000-156865800	Weak transcription	Aorta	Aorta
11	chr3:156855000-156866000	Weak transcription	Ovary	ovary
12	chr3:156855000-156872000	Weak transcription	Right Atrium	heart
13	chr3:156855200-156861800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:156855200-156862000	Weak transcription	Pancreas	Pancrea
15	chr3:156855200-156862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:156855400-156862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:156855400-156862200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:156855400-156862200	Weak transcription	HSMMtube	muscle
19	chr3:156855400-156865400	Weak transcription	Fetal Brain Male	brain
20	chr3:156855400-156865800	Weak transcription	Colonic Mucosa	Colon
21	chr3:156855400-156866000	Weak transcription	Fetal Heart	heart
22	chr3:156855400-156877000	Weak transcription	Gastric	stomach
23	chr3:156855600-156862000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:156855600-156862000	Weak transcription	HMEC	breast
25	chr3:156855600-156862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:156855600-156862200	Weak transcription	K562	blood
27	chr3:156855600-156863200	Weak transcription	NH-A	brain
28	chr3:156855600-156863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:156855600-156863600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:156855600-156864200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:156855600-156865400	Weak transcription	HepG2	liver
32	chr3:156855600-156865800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:156855600-156865800	Weak transcription	NHLF	lung
34	chr3:156855600-156866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:156855600-156867200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:156855800-156862000	Weak transcription	NHEK	skin
37	chr3:156855800-156865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:156855800-156867400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:156856000-156863800	Weak transcription	Stomach Mucosa	stomach
40	chr3:156856000-156870800	Strong transcription	Primary T cells from cord blood	blood
41	chr3:156856000-156874600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:156857200-156864000	Strong transcription	Left Ventricle	heart
43	chr3:156858000-156871200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:156858000-156872000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:156858200-156870400	Strong transcription	Liver	Liver
46	chr3:156858200-156871200	Strong transcription	Adipose Nuclei	Adipose
47	chr3:156858400-156876400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:156858600-156871200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:156858600-156871200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr3:156858600-156872200	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links