Variant report

Variant	rs6557165
Chromosome Location	chr6:150228019-150228020
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150226570..150229723-chr6:150237444..150240125,3	K562	blood:
2	chr6:150182462..150186110-chr6:150225717..150228741,3	MCF-7	breast:
3	chr6:150222304..150224162-chr6:150225800..150228066,2	MCF-7	breast:
4	chr6:150195717..150198563-chr6:150225615..150228061,2	K562	blood:

Variant related genes	Relation type
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10457852	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12204653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12209310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527391	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12528243	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1855572	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1999632	0.94[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1999633	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2342766	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3798763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3922946	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3922947	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4473864	0.97[ASN][1000 genomes]
rs4869755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869767	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4869768	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4870078	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4870110	0.97[ASN][1000 genomes]
rs4870117	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4870118	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5024811	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57894361	0.83[EUR][1000 genomes]
rs6912330	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7452592	0.84[EUR][1000 genomes]
rs7764677	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915140	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9322229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371228	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9383941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397070	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]

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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6557165	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs6557165	NUP43	cis	multi-tissue	Pritchard
rs6557165	RP11-350J20.5	cis	lung	GTEx
rs6557165	RAET1G	cis	Thyroid	GTEx
rs6557165	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs6557165	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs6557165	NUP43	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150222600-150229800	Weak transcription	Pancreas	Pancrea
2	chr6:150226200-150242000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:150226600-150228200	Enhancers	Adipose Nuclei	Adipose
4	chr6:150227200-150229800	Weak transcription	Esophagus	oesophagus
5	chr6:150227600-150228400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:150227800-150228600	Weak transcription	Lung	lung
7	chr6:150227800-150230200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:150227800-150243400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links