Variant report

Variant	rs1427778
Chromosome Location	chr3:140174377-140174378
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	chr3:140173675..140176130-chr3:140184523..140186142,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10935381	0.82[AMR][1000 genomes]
rs10935383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923323	0.82[AMR][1000 genomes]
rs11925150	0.82[AMR][1000 genomes]
rs11926945	0.82[AMR][1000 genomes]
rs12486034	0.82[AMR][1000 genomes]
rs13085384	0.84[AMR][1000 genomes]
rs13092991	0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs1427781	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[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16850245	0.82[AMR][1000 genomes]
rs2114859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35757937	0.82[AMR][1000 genomes]
rs3846016	0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs3909790	0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs3909791	0.82[AMR][1000 genomes]
rs3912204	0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs4142787	0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs4611778	0.84[AMR][1000 genomes]
rs62266407	0.82[AMR][1000 genomes]
rs66934556	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72632309	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9757210	0.82[AMR][1000 genomes]
rs9877176	0.83[CHB][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes]
rs9882815	0.83[CHB][hapmap];0.84[AMR][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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140153600-140178400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:140158200-140189000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:140162000-140185200	Weak transcription	Adipose Nuclei	Adipose
4	chr3:140171200-140174400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:140171600-140181800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:140172200-140178400	Weak transcription	Ovary	ovary
7	chr3:140173200-140174400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:140173800-140175000	Genic enhancers	HSMMtube	muscle
9	chr3:140174000-140174600	Enhancers	Fetal Brain Male	brain
10	chr3:140174000-140175200	Enhancers	Fetal Muscle Leg	muscle
11	chr3:140174000-140175200	Enhancers	Fetal Stomach	stomach
12	chr3:140174200-140175000	Enhancers	Fetal Muscle Trunk	muscle
13	chr3:140174200-140175000	Enhancers	Left Ventricle	heart

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