Variant report

Variant	rs3117320
Chromosome Location	chr6:33350174-33350175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33238834..33242273-chr6:33348728..33351900,3	K562	blood:
2	chr6:33350087..33352952-chr6:33384695..33386243,2	K562	blood:
3	chr6:33254790..33256501-chr6:33349050..33351676,2	K562	blood:
4	chr6:33287030..33291405-chr6:33349040..33354148,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223501	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000112514	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11757273	0.82[ASN][1000 genomes]
rs12204193	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1613451	0.85[ASN][1000 genomes]
rs1755047	0.85[ASN][1000 genomes]
rs2274730	0.89[ASN][1000 genomes]
rs2480487	0.83[ASN][1000 genomes]
rs2743	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2747477	0.81[ASN][1000 genomes]
rs2747479	0.81[ASN][1000 genomes]
rs2772373	0.86[ASN][1000 genomes]
rs2772387	0.82[ASN][1000 genomes]
rs2772390	0.83[ASN][1000 genomes]
rs2772392	0.83[ASN][1000 genomes]
rs3130001	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3130002	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130006	0.84[AMR][1000 genomes]
rs3130007	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130015	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130025	0.83[ASN][1000 genomes]
rs3130274	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130275	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130276	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs371005	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs376006	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs391500	0.88[AMR][1000 genomes]
rs420714	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs442745	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs456993	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459927	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs461887	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs461964	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4620113	0.88[ASN][1000 genomes]
rs465223	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs465474	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs465506	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs465877	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs467065	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66840884	0.81[ASN][1000 genomes]
rs6942045	0.89[AMR][1000 genomes]
rs9278025	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9278029	0.88[AMR][1000 genomes]
rs9357159	0.81[ASN][1000 genomes]
rs9368760	0.84[AMR][1000 genomes]
rs9380355	0.89[ASN][1000 genomes]
rs9461856	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3117320	TAPBP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33341000-33352400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33341200-33358600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:33343800-33350200	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:33343800-33359200	Weak transcription	Right Atrium	heart
5	chr6:33344000-33350200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:33344000-33351800	Weak transcription	Esophagus	oesophagus
7	chr6:33345600-33358800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:33347800-33350200	Enhancers	K562	blood
9	chr6:33348400-33358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:33348600-33352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:33350000-33350200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:33350000-33351200	Enhancers	Placenta	Placenta

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