Variant report

Variant	rs59106803
Chromosome Location	chr2:189253343-189253344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189252210..189254786-chr2:189270636..189272826,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10167709	0.81[ASN][1000 genomes]
rs10174928	0.81[ASN][1000 genomes]
rs10175259	0.82[ASN][1000 genomes]
rs10180222	0.87[ASN][1000 genomes]
rs10180687	0.80[ASN][1000 genomes]
rs10210696	0.80[ASN][1000 genomes]
rs10804020	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931346	0.82[EUR][1000 genomes]
rs10931355	0.81[ASN][1000 genomes]
rs10931356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931359	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12329399	0.81[ASN][1000 genomes]
rs12465164	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12465625	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12469904	0.84[EUR][1000 genomes]
rs12473653	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12473872	0.80[AFR][1000 genomes]
rs12474692	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12611919	0.88[EUR][1000 genomes]
rs12613615	0.84[ASN][1000 genomes]
rs12619361	0.87[ASN][1000 genomes]
rs12624002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693489	0.84[ASN][1000 genomes]
rs12693498	0.81[ASN][1000 genomes]
rs12987194	0.80[ASN][1000 genomes]
rs12990374	0.81[ASN][1000 genomes]
rs13008931	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13014693	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13022513	0.84[EUR][1000 genomes]
rs13389879	0.81[ASN][1000 genomes]
rs34189381	0.88[ASN][1000 genomes]
rs34445909	0.84[EUR][1000 genomes]
rs34778517	0.84[EUR][1000 genomes]
rs35180255	0.88[EUR][1000 genomes]
rs35365782	0.86[EUR][1000 genomes]
rs35964306	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4261684	0.80[ASN][1000 genomes]
rs4349309	0.81[ASN][1000 genomes]
rs4361092	0.80[ASN][1000 genomes]
rs4381753	0.82[EUR][1000 genomes]
rs4402719	0.87[ASN][1000 genomes]
rs4426503	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4430902	0.80[ASN][1000 genomes]
rs4516391	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4564741	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4591312	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4599076	0.84[EUR][1000 genomes]
rs4610010	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4640356	0.80[ASN][1000 genomes]
rs4666759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667215	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667221	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4667222	0.86[EUR][1000 genomes]
rs4992744	0.80[ASN][1000 genomes]
rs60796263	0.81[ASN][1000 genomes]
rs62183206	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183212	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62183213	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434269	0.85[ASN][1000 genomes]
rs6712056	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724636	0.84[EUR][1000 genomes]
rs6724867	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739162	0.81[ASN][1000 genomes]
rs6744629	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6753371	0.84[EUR][1000 genomes]
rs7420700	0.81[ASN][1000 genomes]
rs7425596	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566619	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574262	0.97[ASN][1000 genomes]
rs7585703	0.87[ASN][1000 genomes]
rs7586390	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7593215	0.81[ASN][1000 genomes]
rs7593546	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7598279	0.88[ASN][1000 genomes]
rs7599516	0.87[ASN][1000 genomes]
rs7607063	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59106803	GULP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189245200-189259800	Weak transcription	Gastric	stomach
2	chr2:189247600-189253400	Weak transcription	Left Ventricle	heart
3	chr2:189247600-189259800	Weak transcription	Pancreas	Pancrea
4	chr2:189247800-189259600	Weak transcription	Fetal Heart	heart
5	chr2:189248200-189253800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:189248200-189254800	Weak transcription	HUVEC	blood vessel
7	chr2:189248400-189255400	Weak transcription	Osteobl	bone
8	chr2:189250200-189259800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:189250200-189261000	Weak transcription	Fetal Stomach	stomach
10	chr2:189250400-189259600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:189251000-189253600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:189251000-189253600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:189251000-189255600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:189251000-189258200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:189251000-189259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:189251000-189260000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:189251000-189260000	Weak transcription	Lung	lung
18	chr2:189251000-189260000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:189251000-189285200	Weak transcription	Aorta	Aorta
20	chr2:189251200-189253400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:189251200-189254000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:189251200-189254400	Weak transcription	Ovary	ovary
23	chr2:189251200-189254800	Weak transcription	Fetal Kidney	kidney
24	chr2:189251200-189255600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:189251200-189255600	Weak transcription	Fetal Lung	lung
26	chr2:189251200-189257600	Weak transcription	Fetal Intestine Large	intestine
27	chr2:189251200-189257800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:189251200-189259800	Weak transcription	Placenta	Placenta
29	chr2:189251200-189268400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:189251200-189269000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:189251200-189269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:189251200-189269400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:189251200-189270000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:189251200-189270200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:189251400-189254200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:189251600-189253600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:189251600-189254600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:189251800-189253400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:189251800-189263600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:189252000-189257400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:189252400-189262400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:189253200-189253800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:189253200-189254600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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