Variant report

Variant	rs7411
Chromosome Location	chr1:71529401-71529402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:71528704..71533041-chr1:71544796..71547832,3	MCF-7	breast:
2	chr1:70685786..70687454-chr1:71528741..71531552,2	K562	blood:

Variant related genes	Relation type
ENSG00000228988	Chromatin interaction
ENSG00000229956	Chromatin interaction
ENSG00000116754	Chromatin interaction
ENSG00000132485	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009311	0.81[ASN][1000 genomes]
rs10493481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11209743	0.95[ASN][1000 genomes]
rs11209745	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11209747	0.96[ASN][1000 genomes]
rs1138177	0.84[ASN][1000 genomes]
rs12084460	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12118599	0.81[ASN][1000 genomes]
rs12131265	1.00[JPT][hapmap]
rs12139565	0.85[ASN][1000 genomes]
rs12729268	0.81[ASN][1000 genomes]
rs12748649	0.96[ASN][1000 genomes]
rs1418449	0.85[ASN][1000 genomes]
rs1573061	0.81[ASN][1000 genomes]
rs17090825	0.84[CHB][hapmap]
rs1832900	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1954285	0.81[ASN][1000 genomes]
rs2066371	0.81[ASN][1000 genomes]
rs2639329	0.81[ASN][1000 genomes]
rs2639335	0.81[ASN][1000 genomes]
rs2639338	0.81[ASN][1000 genomes]
rs2796187	0.81[ASN][1000 genomes]
rs2796188	0.81[ASN][1000 genomes]
rs2796189	0.81[ASN][1000 genomes]
rs2796190	0.81[ASN][1000 genomes]
rs2796196	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2796199	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2796201	0.81[ASN][1000 genomes]
rs2796202	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2796203	1.00[JPT][hapmap]
rs2817869	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272572	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4367753	0.88[ASN][1000 genomes]
rs4397614	0.81[ASN][1000 genomes]
rs4425938	0.81[ASN][1000 genomes]
rs66461782	0.84[ASN][1000 genomes]
rs6680193	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7516464	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7519104	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs7556111	0.88[ASN][1000 genomes]
rs880098	1.00[ASN][1000 genomes]
rs952337	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7411	PTGER3	cis	uninvolved skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71513600-71533600	Weak transcription	Lung	lung
2	chr1:71514000-71530600	Weak transcription	Ovary	ovary
3	chr1:71514000-71533600	Weak transcription	Pancreas	Pancrea
4	chr1:71514000-71533600	Weak transcription	Right Ventricle	heart
5	chr1:71514200-71533600	Weak transcription	Spleen	Spleen
6	chr1:71515800-71541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:71519000-71530200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:71519200-71533400	Weak transcription	Fetal Intestine Small	intestine
9	chr1:71520000-71536800	Weak transcription	Aorta	Aorta
10	chr1:71520400-71533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:71520400-71534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:71520600-71533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:71520600-71544600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:71521000-71529800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:71521200-71533600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:71521400-71530400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:71521400-71544200	Strong transcription	Adipose Nuclei	Adipose
18	chr1:71521600-71536800	Weak transcription	Stomach Mucosa	stomach
19	chr1:71521800-71530400	Weak transcription	Small Intestine	intestine
20	chr1:71521800-71544600	Strong transcription	HSMM	muscle
21	chr1:71522000-71534400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:71522000-71543800	Strong transcription	Primary B cells from cord blood	blood
23	chr1:71522000-71544200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:71522000-71544200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:71522000-71544200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:71522000-71544400	Strong transcription	HMEC	breast
27	chr1:71522200-71532600	Strong transcription	GM12878-XiMat	blood
28	chr1:71522200-71534000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:71522200-71540800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:71522200-71544200	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr1:71522200-71544600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:71522400-71530200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:71522400-71544200	Strong transcription	Liver	Liver
34	chr1:71522600-71532800	Strong transcription	Primary T cells from cord blood	blood
35	chr1:71522600-71533400	Weak transcription	Fetal Stomach	stomach
36	chr1:71522600-71544200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:71522600-71544200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:71522600-71544400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:71522600-71544400	Strong transcription	NH-A	brain
40	chr1:71522800-71540400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:71522800-71544400	Strong transcription	Fetal Thymus	thymus
42	chr1:71522800-71544600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:71522800-71544600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:71523000-71531600	Strong transcription	A549	lung
45	chr1:71523000-71543800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:71523000-71544400	Strong transcription	Osteobl	bone
47	chr1:71523000-71544600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:71523000-71544600	Strong transcription	Placenta	Placenta
49	chr1:71523200-71540600	Strong transcription	Dnd41	blood
50	chr1:71523200-71542800	Strong transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links