Variant report

Variant	rs6561461
Chromosome Location	chr13:49118569-49118570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49106673..49108535-chr13:49114144..49118573,5	MCF-7	breast:
2	chr13:49113085..49114630-chr13:49116071..49118855,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136161	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1547660	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1926595	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926596	0.91[ASN][1000 genomes]
rs1926597	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198564	0.85[ASN][1000 genomes]
rs198568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs198574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs198575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs198609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs198610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs198622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2274400	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs28414460	0.91[ASN][1000 genomes]
rs2854353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28646083	0.91[ASN][1000 genomes]
rs28674973	0.84[ASN][1000 genomes]
rs3092888	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3092898	0.88[ASN][1000 genomes]
rs3092899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3751380	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.97[ASN][1000 genomes]
rs398158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs403390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs406098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs4151456	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs4151474	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4151525	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4151601	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs425834	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs427686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs449268	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs61074776	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561465	1.00[CEU][hapmap]
rs7325962	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs7329039	1.00[ASN][1000 genomes]
rs7329865	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs73486867	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495016	0.88[ASN][1000 genomes]
rs7985825	1.00[ASN][1000 genomes]
rs7987935	0.91[ASN][1000 genomes]
rs7992129	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995216	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7996186	0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7996402	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8001241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316385	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316386	0.85[TSI][hapmap]
rs9316396	1.00[TSI][hapmap]
rs9316401	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331959	0.91[ASN][1000 genomes]
rs9331965	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9331973	0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9332054	0.94[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9591172	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591177	0.98[ASN][1000 genomes]
rs9591178	1.00[ASN][1000 genomes]
rs9595931	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6561461	RCBTB2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49117200-49124800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:49117400-49118600	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:49117400-49118600	Weak transcription	Psoas Muscle	Psoas
4	chr13:49117400-49119000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:49117400-49121800	Weak transcription	Liver	Liver
6	chr13:49117600-49118800	Weak transcription	HepG2	liver
7	chr13:49117600-49119800	Weak transcription	Adipose Nuclei	Adipose
8	chr13:49117600-49120400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr13:49117600-49120600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr13:49117600-49123200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:49118400-49118600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr13:49118400-49124000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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