Variant report

Variant	rs6098099
Chromosome Location	chr20:53208593-53208594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53203687..53205886-chr20:53207596..53209815,3	MCF-7	breast:
2	chr20:53208453..53209976-chr20:53229452..53231324,2	MCF-7	breast:
3	chr20:53201468..53203099-chr20:53207477..53210078,2	MCF-7	breast:
4	chr20:53156247..53159030-chr20:53207905..53210623,2	MCF-7	breast:
5	chr20:52823541..52825305-chr20:53206836..53209645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10154005	0.85[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs10485784	0.85[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13433172	0.84[AMR][1000 genomes]
rs16999893	0.85[CEU][hapmap]
rs17327539	0.96[EUR][1000 genomes]
rs2169707	0.84[EUR][1000 genomes]
rs55705559	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55960128	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56138015	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56294816	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56371656	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57120787	0.80[AMR][1000 genomes]
rs6014059	1.00[GIH][hapmap]
rs6014066	0.83[EUR][1000 genomes]
rs6014067	0.84[EUR][1000 genomes]
rs6014073	0.83[EUR][1000 genomes]
rs6014074	0.84[EUR][1000 genomes]
rs6014075	0.84[EUR][1000 genomes]
rs6014076	0.84[EUR][1000 genomes]
rs6014087	0.87[AMR][1000 genomes]
rs6014089	0.85[CEU][hapmap];0.87[AMR][1000 genomes]
rs6014098	0.85[CEU][hapmap]
rs6023244	1.00[GIH][hapmap]
rs6023245	1.00[GIH][hapmap]
rs6023251	1.00[GIH][hapmap]
rs6023367	0.85[LWK][hapmap]
rs6023382	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs6023383	1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs6023384	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6023385	0.84[EUR][1000 genomes]
rs6023386	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6023387	0.84[EUR][1000 genomes]
rs6023388	0.84[EUR][1000 genomes]
rs6023396	0.84[EUR][1000 genomes]
rs6023422	0.87[AMR][1000 genomes]
rs6068930	1.00[GIH][hapmap]
rs6091886	1.00[GIH][hapmap]
rs6091925	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6091933	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6098093	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6098104	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6098111	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6098116	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6098118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6098123	0.84[AMR][1000 genomes]
rs6098130	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs62214427	0.90[EUR][1000 genomes]
rs62214433	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67907005	0.96[EUR][1000 genomes]
rs73140147	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73144055	0.84[AMR][1000 genomes]
rs73144063	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73144072	0.88[EUR][1000 genomes]
rs73144079	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73144086	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73146053	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73146055	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs873078	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53202000-53211800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr20:53202200-53230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:53203800-53210200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
5	chr20:53206400-53208800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:53206400-53226600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:53206600-53214800	Weak transcription	Aorta	Aorta
8	chr20:53206600-53216600	Weak transcription	Fetal Brain Female	brain
9	chr20:53207200-53217000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr20:53208000-53209000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:53208200-53208800	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links