Variant report

Variant	rs621942
Chromosome Location	chr11:85783738-85783739
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85779081..85782313-chr11:85782461..85788148,6	MCF-7	breast:
2	chr11:85783105..85786132-chr11:85791700..85793903,3	MCF-7	breast:
3	chr11:85773042..85775318-chr11:85782824..85785081,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1214410	0.81[EUR][1000 genomes]
rs1941375	0.92[ASW][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs3016329	0.81[EUR][1000 genomes]
rs490507	0.95[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs510566	0.86[EUR][1000 genomes]
rs545213	0.89[EUR][1000 genomes]
rs547807	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs583463	0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs588992	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs590055	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs615887	0.84[ASW][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.81[YRI][hapmap]
rs622110	0.91[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap]
rs622876	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628161	0.84[EUR][1000 genomes]
rs636848	0.95[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs637193	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs638509	0.89[YRI][hapmap]
rs655726	0.84[EUR][1000 genomes]
rs6592272	0.91[CHB][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap]
rs664596	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs664629	0.92[ASW][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap]
rs669336	0.84[ASW][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap]
rs681041	0.92[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs682058	0.88[EUR][1000 genomes]
rs787928	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Tourette syndrome	22889924	GWAS catalog

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85780800-85784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:85781000-85784000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:85781200-85783800	Enhancers	NHDF-Ad	bronchial
4	chr11:85781200-85784000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:85781400-85783800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:85781400-85796000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:85781600-85784400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:85781800-85785600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:85782000-85783800	Enhancers	K562	blood
10	chr11:85782000-85783800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:85782000-85784800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:85782400-85785200	Weak transcription	Placenta	Placenta
13	chr11:85783600-85785000	Weak transcription	HSMM	muscle

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