Variant report

Variant	rs6786523
Chromosome Location	chr3:50524221-50524222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1107265	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap]
rs12490042	0.83[CEU][hapmap]
rs12494849	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087550	0.83[CEU][hapmap]
rs1467913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467914	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073499	0.80[ASW][hapmap]
rs2233474	0.86[ASW][hapmap]
rs2236953	0.83[CEU][hapmap]
rs2236954	0.94[CEU][hapmap];0.87[GIH][hapmap]
rs2236955	0.89[CEU][hapmap]
rs2236956	0.83[CEU][hapmap]
rs2236957	0.89[CEU][hapmap]
rs2236958	0.87[CEU][hapmap]
rs2236959	0.89[CEU][hapmap]
rs2236961	0.82[CEU][hapmap]
rs2236963	0.83[CEU][hapmap]
rs2236964	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236965	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236967	0.83[CEU][hapmap]
rs2236968	0.83[CEU][hapmap]
rs2236973	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236975	0.83[CEU][hapmap]
rs2236979	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap]
rs2236981	0.83[EUR][1000 genomes]
rs2236984	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes]
rs2236987	0.80[ASW][hapmap];0.89[CEU][hapmap];0.90[CHD][hapmap];0.81[EUR][1000 genomes]
rs2236988	0.83[CEU][hapmap]
rs2282752	0.94[CEU][hapmap]
rs2282753	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap]
rs2282754	0.89[CEU][hapmap];0.87[GIH][hapmap]
rs2282756	0.83[CEU][hapmap]
rs2282758	0.83[CEU][hapmap]
rs2282762	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2298955	0.89[CEU][hapmap];0.87[GIH][hapmap]
rs34704833	0.81[EUR][1000 genomes]
rs34762184	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs34860383	0.81[EUR][1000 genomes]
rs35053615	0.84[EUR][1000 genomes]
rs35198275	0.84[EUR][1000 genomes]
rs35335661	0.84[EUR][1000 genomes]
rs35684775	0.84[EUR][1000 genomes]
rs35829757	0.84[EUR][1000 genomes]
rs35908181	0.81[EUR][1000 genomes]
rs35986136	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs36059704	0.84[EUR][1000 genomes]
rs4688719	0.88[CEU][hapmap]
rs57361338	0.81[EUR][1000 genomes]
rs58432784	0.84[EUR][1000 genomes]
rs61018691	0.81[EUR][1000 genomes]
rs61423002	0.81[EUR][1000 genomes]
rs6446206	0.81[EUR][1000 genomes]
rs6787890	0.83[CEU][hapmap]
rs6792502	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6807916	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs71326934	0.84[EUR][1000 genomes]
rs734767	0.89[CEU][hapmap];0.87[GIH][hapmap]
rs73835511	0.84[EUR][1000 genomes]
rs73835517	0.81[EUR][1000 genomes]
rs743756	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs743757	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs743856	0.85[AMR][1000 genomes]
rs743857	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes]
rs7613931	0.84[EUR][1000 genomes]
rs762895	0.83[CEU][hapmap]
rs762897	0.88[CEU][hapmap]
rs762898	0.83[CEU][hapmap]
rs763030	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916217	0.83[CEU][hapmap]
rs929047	0.83[CEU][hapmap]
rs9835537	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap]
rs9867588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	esv998611	chr3:50519293-50526732	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6786523	CAMP	cis	cerebellum	SCAN
rs6786523	ALS2CL	cis	parietal	SCAN
rs6786523	APEH	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50492600-50528400	Weak transcription	Gastric	stomach
2	chr3:50513000-50527400	Weak transcription	Right Atrium	heart
3	chr3:50519800-50524600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:50520000-50524600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:50520000-50524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:50520200-50527800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:50520400-50530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:50520800-50528400	Weak transcription	Spleen	Spleen
9	chr3:50522000-50525600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:50522000-50533600	Weak transcription	Lung	lung
11	chr3:50522600-50524800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:50522600-50524800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:50522600-50525000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:50522800-50528000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:50523200-50525400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:50523800-50527200	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:50524000-50525600	Enhancers	Fetal Thymus	thymus
18	chr3:50524200-50525800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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