Variant report

Variant	rs9838521
Chromosome Location	chr3:140078489-140078490
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	chr3:140077666..140079764-chr3:140083559..140086376,4	MCF-7	breast:
2	chr3:140078397..140079800-chr3:140217706..140218666,5	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006877	0.88[CHB][hapmap]
rs1026773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1026774	0.93[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1026775	0.82[EUR][1000 genomes]
rs1026776	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1026777	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026778	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1026779	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11707077	0.93[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11714825	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11714842	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11715839	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719018	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11719055	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11719890	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13319247	0.85[EUR][1000 genomes]
rs1383016	1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345403	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1871497	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs3943277	0.82[EUR][1000 genomes]
rs3947733	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6414346	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6766541	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6770286	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6770610	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6777920	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6789020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790930	0.93[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6794692	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6794805	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6795544	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6795632	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6810326	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs7623769	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7630996	0.88[CHB][hapmap]
rs9289603	0.88[CHB][hapmap]
rs9813628	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9814193	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9832534	0.88[CHB][hapmap]
rs9837886	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874598	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]

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:6 , 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	chr3:140073800-140085000	Weak transcription	HSMMtube	muscle
3	chr3:140076800-140079000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:140077000-140082400	Weak transcription	Ovary	ovary
5	chr3:140078000-140079000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:140078000-140079400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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