Variant report

Variant	rs6600954
Chromosome Location	chr5:178217553-178217554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178217515..178219756-chr5:178222476..178225165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250420	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11952919	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11952924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11956290	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957056	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655252	0.85[ASN][1000 genomes]
rs12658342	0.95[ASN][1000 genomes]
rs13174784	0.89[CHB][hapmap]
rs34180938	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4701068	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61469010	0.93[ASN][1000 genomes]
rs6600955	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6600956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600957	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6862477	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874045	0.95[ASN][1000 genomes]
rs73341509	0.93[ASN][1000 genomes]
rs73341510	0.92[ASN][1000 genomes]
rs73341513	0.95[ASN][1000 genomes]
rs73341521	0.95[ASN][1000 genomes]
rs73341529	0.95[ASN][1000 genomes]
rs73341553	0.85[ASN][1000 genomes]
rs7444422	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7447672	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711944	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7713247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720287	0.93[ASN][1000 genomes]
rs7722026	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7725396	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7733056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv462573	chr5:178180299-178241495	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv600452	chr5:178180299-178241495	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178166600-178224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:178206400-178217600	Weak transcription	Gastric	stomach
3	chr5:178215800-178217600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:178215800-178217800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:178216600-178217800	Enhancers	Placenta	Placenta
6	chr5:178216600-178218000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:178216600-178218000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr5:178216800-178218000	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr5:178217000-178217600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:178217200-178217600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:178217400-178218000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:178217400-178218000	Enhancers	Esophagus	oesophagus

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