Variant report

Variant	rs4911293
Chromosome Location	chr20:31653782-31653783
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:31648171..31652002-chr20:31652342..31655282,4	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1022676	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs11696307	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs11696310	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs11699009	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs13044428	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs1972218	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs1998113	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[TSI][hapmap]
rs2057261	0.87[CHB][hapmap];0.82[GIH][hapmap]
rs2057262	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs2070319	0.87[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap]
rs2070320	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs2070325	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs2073325	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs2093067	0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs221982	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs2424936	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs2424940	0.84[CHB][hapmap];0.82[AFR][1000 genomes]
rs2424942	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs2424945	0.93[CHB][hapmap]
rs2424946	0.93[CHB][hapmap]
rs2424947	0.93[CHB][hapmap]
rs2424953	0.87[CHB][hapmap]
rs2889732	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs372054	0.93[ASN][1000 genomes]
rs398444	0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4911286	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap]
rs4911287	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs4911290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4911291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4911292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4911295	0.94[ASN][1000 genomes]
rs4911296	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4911297	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6057715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6057717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6059052	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6059058	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6059067	0.85[ASN][1000 genomes]
rs6059069	1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6059079	0.87[CHB][hapmap];0.80[GIH][hapmap]
rs6087440	0.80[AMR][1000 genomes]
rs6087441	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6088082	0.86[CEU][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6088084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6088085	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6088091	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6141362	0.91[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6141871	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs6141876	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6141877	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs761935	0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs761936	0.92[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056411	chr20:31057037-31942835	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2758519	chr20:31495807-31748166	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758792	chr20:31495807-31748166	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv3352	chr20:31609939-31654756	Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv1062857	chr20:31620361-31654093	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4911293	TTLL9	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:31643800-31657000	Weak transcription	Spleen	Spleen
2	chr20:31650600-31655200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:31650800-31658400	Weak transcription	Right Atrium	heart
4	chr20:31651400-31655600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:31653400-31654000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr20:31653600-31654000	Bivalent Enhancer	HepG2	liver
7	chr20:31653600-31654200	Enhancers	NHEK	skin

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