Variant report

Variant	rs6135109
Chromosome Location	chr20:14260281-14260282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11087084	0.92[JPT][hapmap]
rs12329405	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs12624446	0.85[EUR][1000 genomes]
rs1570486	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs204637	0.85[JPT][hapmap]
rs2145560	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2208454	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208456	0.92[JPT][hapmap]
rs2327846	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2327847	0.86[ASN][1000 genomes]
rs3789335	0.84[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs6033952	0.85[JPT][hapmap]
rs6105236	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6105243	0.92[JPT][hapmap]
rs6105245	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6105246	0.85[JPT][hapmap]
rs6105247	0.92[JPT][hapmap]
rs6105250	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6110208	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6110220	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6110235	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6110242	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6110247	0.86[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6110251	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6110252	0.84[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs6110255	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs6110259	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs6110263	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6110264	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs6131564	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6135108	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135124	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6135125	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6135127	0.85[JPT][hapmap]
rs6135128	0.84[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs743216	0.84[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs8126410	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv532514	chr20:14097780-14288315	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv458872	chr20:14189779-14317390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv470540	chr20:14189779-14317390	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv585439	chr20:14189779-14317390	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1066105	chr20:14201909-14272115	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14258600-14261600	Enhancers	HMEC	breast
2	chr20:14259000-14263400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:14259200-14261000	Weak transcription	NHEK	skin
4	chr20:14260000-14263200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links