Variant report

Variant	rs6790568
Chromosome Location	chr3:49835450-49835451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49828367..49831319-chr3:49832750..49837135,3	MCF-7	breast:
2	chr3:49822443..49824748-chr3:49834059..49836824,2	K562	blood:
3	chr3:49835114..49838114-chr3:49838714..49841176,3	K562	blood:
4	chr3:49832962..49835911-chr3:49836765..49838796,2	K562	blood:
5	chr3:49828847..49830449-chr3:49834331..49837009,2	K562	blood:

Variant related genes	Relation type
ENSG00000187492	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130217	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1491985	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1799844	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1996663	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1996664	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28535523	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35129566	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55997059	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58339610	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59357103	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59684465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61557789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260663	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260720	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260723	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62262722	0.95[EUR][1000 genomes]
rs62262730	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6804970	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809879	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613603	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620848	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621797	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628207	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7637711	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649428	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9829155	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9835157	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9836756	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851651	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870755	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870858	0.93[AMR][1000 genomes];0.94[EUR][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6790568	RNF123	cis	Artery Tibial	GTEx
rs6790568	AMT	cis	Thyroid	GTEx
rs6790568	AMT	cis	lung	GTEx
rs6790568	NICN1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49825200-49836400	Weak transcription	Esophagus	oesophagus
2	chr3:49825600-49840000	Weak transcription	Spleen	Spleen
3	chr3:49833200-49838800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49833400-49836800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:49833400-49838800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49833600-49836600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:49835200-49839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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