Variant report

Variant	rs299384
Chromosome Location	chr5:17368172-17368173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10074496	0.92[EUR][1000 genomes]
rs10462609	0.92[EUR][1000 genomes]
rs11950287	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13355635	0.92[EUR][1000 genomes]
rs16869688	0.81[GIH][hapmap]
rs16869690	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs182441	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827400	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2134241	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2134242	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2173968	0.84[CEU][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2454946	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2459811	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2650923	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650935	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2650936	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650937	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650938	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650939	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650940	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650942	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650943	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650944	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2650945	0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652638	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652639	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652640	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652641	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652643	0.89[CEU][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652644	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652645	0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652646	0.80[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2652647	0.83[CEU][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2652648	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28476505	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs298530	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298532	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298534	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298535	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298536	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298546	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298547	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298548	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298550	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298558	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs298559	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs298560	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs298562	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs299385	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299386	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56663279	0.93[EUR][1000 genomes]
rs56705013	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58062922	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58468495	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6862515	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73052871	0.92[EUR][1000 genomes]
rs73052881	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73052887	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73052888	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73052898	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73052901	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73054809	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73054823	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7719794	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv1793466	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	esv1801170	chr5:17364700-17721569	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	esv1820519	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	esv1824831	chr5:17364700-17721569	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	esv1827359	chr5:17364700-17721569	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	esv1828062	chr5:17364700-17721569	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv427713	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv428464	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	esv2757986	chr5:17364700-17936404	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	esv2759328	chr5:17364700-17936404	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17362200-17375200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:17365400-17368200	Enhancers	Fetal Brain Male	brain
3	chr5:17366000-17374600	Weak transcription	Fetal Brain Female	brain
4	chr5:17366400-17368600	Enhancers	Brain Germinal Matrix	brain
5	chr5:17366400-17373600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:17366800-17368400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:17367000-17368200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:17367000-17368400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr5:17367000-17368400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr5:17367000-17368400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr5:17367000-17368600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr5:17367200-17368400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:17367200-17368400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:17367200-17368400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:17367200-17373600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:17367600-17368400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:17367800-17368200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:17367800-17370200	Strong transcription	A549	lung
19	chr5:17368000-17368400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:17368000-17368600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:17368000-17369400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:17368000-17373400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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