Variant report

Variant	rs27657
Chromosome Location	chr5:89847869-89847870
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	chr5:89826971..89828828-chr5:89846994..89849813,2	MCF-7	breast:
2	chr5:89843926..89847301-chr5:89847464..89849372,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11952742	0.84[LWK][hapmap]
rs1344030	0.84[LWK][hapmap]
rs154559	0.81[MEX][hapmap]
rs154562	0.91[AMR][1000 genomes]
rs154563	0.81[JPT][hapmap]
rs154571	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16868901	0.84[LWK][hapmap]
rs171629	0.92[AMR][1000 genomes]
rs173660	1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs189691	0.89[AMR][1000 genomes]
rs2247158	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs250367	1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs2562523	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs257855	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27202	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27601	0.83[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs27602	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37480	0.83[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs37482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916807	0.81[LWK][hapmap]
rs4916809	0.82[ASW][hapmap]
rs58598764	0.83[AMR][1000 genomes]
rs7707357	0.84[LWK][hapmap]
rs7709691	0.87[LWK][hapmap]
rs7722900	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs950692	0.91[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89843400-89849600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:89843400-89852800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:89843400-89853200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:89844200-89848000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:89844200-89853200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:89844200-89853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:89844400-89849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:89844400-89849600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:89844400-89849600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:89844400-89853200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:89844600-89849400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:89844600-89849600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:89844800-89849400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:89844800-89849400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:89845200-89849800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:89845800-89848000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr5:89845800-89849200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:89846200-89853200	Weak transcription	K562	blood
19	chr5:89847600-89848200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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