Variant report

Variant	rs1564397
Chromosome Location	chr3:140070453-140070454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140068811..140071526-chr3:140072491..140074846,2	MCF-7	breast:
2	chr3:140058084..140060936-chr3:140070317..140072868,2	K562	blood:
3	chr3:140062953..140066461-chr3:140067922..140071078,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1006877	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1006878	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs1154765	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1154766	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11706485	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11717522	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11917245	1.00[JPT][hapmap]
rs13319247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1383020	1.00[JPT][hapmap]
rs1479852	0.84[CHB][hapmap]
rs1479866	1.00[JPT][hapmap]
rs1479879	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1564395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17345403	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1871497	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061927	1.00[JPT][hapmap]
rs2061929	1.00[JPT][hapmap]
rs2086330	1.00[JPT][hapmap]
rs3943277	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs3947733	0.84[EUR][1000 genomes]
rs4076964	1.00[JPT][hapmap]
rs4362682	1.00[JPT][hapmap]
rs4365587	1.00[JPT][hapmap]
rs4371479	1.00[JPT][hapmap]
rs4438621	1.00[JPT][hapmap]
rs4518083	1.00[JPT][hapmap]
rs4583599	1.00[JPT][hapmap]
rs4683484	1.00[JPT][hapmap]
rs4683488	1.00[JPT][hapmap]
rs6414346	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6762256	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765087	1.00[JPT][hapmap]
rs6766533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6766541	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6771702	0.84[CHB][hapmap]
rs6786128	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6797652	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6810326	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7431715	1.00[JPT][hapmap]
rs7610675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611205	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7630996	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7631243	0.84[EUR][1000 genomes]
rs7653676	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9811609	1.00[JPT][hapmap]
rs9817769	1.00[JPT][hapmap]
rs9832534	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs9837940	0.84[EUR][1000 genomes]
rs9871764	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs987486	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs995578	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv829740	chr3:139925767-140106169	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv460867	chr3:140007294-140180563	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv591861	chr3:140007294-140180563	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv818169	chr3:140014763-140182046	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1001430	chr3:140016999-140186498	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv998953	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv536731	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv829741	chr3:140021063-140183294	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1004500	chr3:140021594-140189148	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140061800-140084800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:140068800-140071800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:140069000-140076600	Weak transcription	Ovary	ovary
4	chr3:140070200-140071800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:140070200-140071800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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