Variant report

Variant	rs929047
Chromosome Location	chr3:50503170-50503171
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	chr3:50497151..50499285-chr3:50501745..50504629,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1107265	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs11130250	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490042	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12492113	0.82[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494849	0.83[CEU][hapmap]
rs13087550	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13091933	0.83[CEU][hapmap]
rs13099869	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1467913	0.83[CEU][hapmap]
rs1467914	0.83[CEU][hapmap]
rs2027854	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236950	0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs2236953	1.00[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2236954	0.94[CEU][hapmap]
rs2236955	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs2236956	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236957	0.94[CEU][hapmap]
rs2236958	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236959	0.94[CEU][hapmap]
rs2236961	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236962	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236963	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236964	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2236965	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2236967	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236968	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236971	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236973	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2236975	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236979	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs2236981	0.83[EUR][1000 genomes]
rs2236983	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236984	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2236987	0.94[CEU][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2236988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282752	0.94[CEU][hapmap]
rs2282753	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs2282754	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs2282756	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2282758	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2282760	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2282762	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2298955	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs34762184	0.88[CEU][hapmap]
rs35986136	0.88[CEU][hapmap]
rs4688719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688720	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs628081	0.83[CEU][hapmap]
rs6446206	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6786523	0.83[CEU][hapmap]
rs6787890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6788459	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792502	0.83[CEU][hapmap]
rs6807916	0.88[CEU][hapmap]
rs71326932	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs734767	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs743756	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs743757	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs743857	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs762895	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs762897	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs762898	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs763030	0.83[CEU][hapmap]
rs8180034	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs916217	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9835537	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs9867588	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
5	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
7	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
8	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs929047	HYAL2	cis	parietal	SCAN
rs929047	CAMKV	cis	parietal	SCAN
rs929047	RASSF1	cis	lymphoblastoid	seeQTL
rs929047	APEH	cis	cerebellum	SCAN
rs929047	CAMP	cis	cerebellum	SCAN
rs929047	TRAIP	cis	parietal	SCAN
rs929047	PARP3	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50488600-50511200	Weak transcription	Lung	lung
2	chr3:50492600-50528400	Weak transcription	Gastric	stomach
3	chr3:50493000-50518600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:50493800-50518800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:50496400-50511600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:50501000-50503600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:50501200-50503200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:50502200-50503200	Enhancers	Brain Germinal Matrix	brain
9	chr3:50502200-50510800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:50502600-50509000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:50502600-50509600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:50502600-50515600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:50502800-50520800	Weak transcription	Brain Anterior Caudate	brain

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