Variant report

Variant	rs6083125
Chromosome Location	chr20:23423097-23423098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23415648..23417559-chr20:23421207..23423158,2	MCF-7	breast:
2	chr20:23422636..23423138-chr9:129901794..129902375,2	MCF-7	breast:
3	chr20:23422547..23423488-chr20:23586916..23587742,4	K562	blood:
4	chr20:23329921..23332820-chr20:23421116..23423226,2	MCF-7	breast:
5	chr20:23421799..23423146-chr20:23586414..23588198,22	MCF-7	breast:
6	chr20:23415427..23417677-chr20:23422614..23424382,2	K562	blood:
7	chr20:23422153..23424654-chr20:23586384..23588911,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234832	Chromatin interaction
ENSG00000132661	Chromatin interaction
ENSG00000173335	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11908625	1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1203994	0.85[ASN][1000 genomes]
rs2281433	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6036387	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6036388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6036393	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6036394	0.81[ASN][1000 genomes]
rs6036395	0.81[ASN][1000 genomes]
rs6036396	0.81[ASN][1000 genomes]
rs6036400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6036402	1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs6048724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048726	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6048727	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048748	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6048749	0.81[ASN][1000 genomes]
rs6048751	0.81[ASN][1000 genomes]
rs6048764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6048773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6048780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6048782	0.96[ASN][1000 genomes]
rs6048783	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6048785	0.93[ASN][1000 genomes]
rs6048787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6048789	0.96[ASN][1000 genomes]
rs6048791	0.96[ASN][1000 genomes]
rs6048792	0.96[ASN][1000 genomes]
rs6048793	0.96[ASN][1000 genomes]
rs6048794	0.94[ASN][1000 genomes]
rs6076052	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6076060	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6076061	0.81[ASN][1000 genomes]
rs6076069	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6083082	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6083091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6083109	0.96[ASN][1000 genomes]
rs6083117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6083120	0.96[ASN][1000 genomes]
rs6106650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6106652	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6114053	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6114078	0.96[ASN][1000 genomes]
rs6114086	1.00[CHD][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73303309	0.89[ASN][1000 genomes]
rs73319497	0.81[ASN][1000 genomes]
rs7361799	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8119387	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23417200-23434800	Weak transcription	Gastric	stomach
2	chr20:23417800-23441000	Weak transcription	Right Atrium	heart
3	chr20:23421200-23427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr20:23422400-23423600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr20:23422400-23426400	Enhancers	Fetal Thymus	thymus
6	chr20:23422800-23423200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr20:23422800-23423400	Enhancers	NHDF-Ad	bronchial
8	chr20:23422800-23423800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:23423000-23432200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links