Variant report

Variant	rs287502
Chromosome Location	chr13:91806965-91806966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:91799328..91800951-chr13:91805313..91807967,2	MCF-7	breast:
2	chr13:91774794..91777277-chr13:91806705..91809687,2	K562	blood:
3	chr13:91799320..91801557-chr13:91805250..91808101,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1020800	0.82[EUR][1000 genomes]
rs1020801	0.82[EUR][1000 genomes]
rs1174782	0.85[EUR][1000 genomes]
rs1174784	0.82[EUR][1000 genomes]
rs1332218	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs148771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs167003	0.93[EUR][1000 genomes]
rs16952571	0.93[EUR][1000 genomes]
rs287490	0.94[EUR][1000 genomes]
rs287491	0.92[EUR][1000 genomes]
rs287492	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs287493	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs287494	0.96[EUR][1000 genomes]
rs287495	0.95[EUR][1000 genomes]
rs287496	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287497	0.93[EUR][1000 genomes]
rs287498	0.93[EUR][1000 genomes]
rs287499	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287500	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287501	0.96[EUR][1000 genomes]
rs287504	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287505	0.96[EUR][1000 genomes]
rs287506	0.94[EUR][1000 genomes]
rs287508	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287509	0.94[EUR][1000 genomes]
rs287510	0.94[EUR][1000 genomes]
rs287511	0.94[EUR][1000 genomes]
rs287512	0.94[EUR][1000 genomes]
rs287513	0.94[EUR][1000 genomes]
rs287514	0.96[EUR][1000 genomes]
rs287515	0.94[EUR][1000 genomes]
rs287516	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287517	0.93[EUR][1000 genomes]
rs287518	0.93[EUR][1000 genomes]
rs287522	0.93[EUR][1000 genomes]
rs287523	0.93[EUR][1000 genomes]
rs287524	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287525	0.89[EUR][1000 genomes]
rs287526	0.93[EUR][1000 genomes]
rs287527	0.95[EUR][1000 genomes]
rs287528	0.93[EUR][1000 genomes]
rs287529	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs287533	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs287535	0.83[EUR][1000 genomes]
rs3764129	0.85[EUR][1000 genomes]
rs481037	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs492117	0.82[EUR][1000 genomes]
rs504180	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs505160	0.82[EUR][1000 genomes]
rs506173	0.82[EUR][1000 genomes]
rs506238	0.82[EUR][1000 genomes]
rs512524	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs515029	0.82[EUR][1000 genomes]
rs515097	0.82[EUR][1000 genomes]
rs515850	0.82[EUR][1000 genomes]
rs536365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539504	0.82[EUR][1000 genomes]
rs543567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544464	0.82[EUR][1000 genomes]
rs549865	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558827	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568455	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs568694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571202	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs582256	0.93[EUR][1000 genomes]
rs583053	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs612195	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs613553	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs620620	0.85[EUR][1000 genomes]
rs622426	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs623637	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs644953	0.82[EUR][1000 genomes]
rs647785	0.82[EUR][1000 genomes]
rs650892	0.81[EUR][1000 genomes]
rs657464	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs665530	0.81[EUR][1000 genomes]
rs684050	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs693721	0.82[EUR][1000 genomes]
rs7324853	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs76384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs922083	0.82[EUR][1000 genomes]
rs9515887	0.93[EUR][1000 genomes]
rs9523263	0.82[EUR][1000 genomes]
rs9560762	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932206	chr13:91370888-91878374	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
4	nsv900880	chr13:91625722-91848290	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
6	nsv900881	chr13:91704312-91829940	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
8	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
9	nsv832678	chr13:91771619-91932241	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs287502	GPC6	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:91796800-91822600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:91799000-91809400	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:91805400-91814600	Weak transcription	Pancreas	Pancrea
4	chr13:91805400-91821600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:91805600-91807200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr13:91805600-91807400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr13:91805600-91807800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr13:91805600-91808200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr13:91805600-91808200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:91805800-91807800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr13:91806000-91807800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:91806000-91808000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:91806400-91807200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr13:91806400-91812000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:91806600-91807000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:91806600-91808200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr13:91806800-91807000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr13:91806800-91807000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
19	chr13:91806800-91807400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:91806800-91807800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr13:91806800-91807800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:91806800-91807800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr13:91806800-91808200	Enhancers	H9 Cell Line	embryonic stem cell
24	chr13:91806800-91808200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:91806800-91808200	Enhancers	Primary hematopoietic stem cells	blood
26	chr13:91806800-91808200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr13:91806800-91808200	Enhancers	Fetal Kidney	kidney
28	chr13:91806800-91808200	Enhancers	Placenta	Placenta
29	chr13:91806800-91809000	Enhancers	Fetal Intestine Large	intestine

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