Variant report

Variant	rs1678658
Chromosome Location	chr6:38744087-38744088
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38742135..38744348-chr6:38746866..38748899,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12173602	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1612377	0.82[ASN][1000 genomes]
rs1615744	0.82[ASN][1000 genomes]
rs1678639	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1678642	0.85[ASN][1000 genomes]
rs1678643	0.85[ASN][1000 genomes]
rs1678652	0.86[ASN][1000 genomes]
rs1678653	0.86[ASN][1000 genomes]
rs1678654	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678655	0.86[ASN][1000 genomes]
rs1678656	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678659	0.86[ASN][1000 genomes]
rs1678662	0.86[ASN][1000 genomes]
rs1678663	0.86[ASN][1000 genomes]
rs1678664	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1678672	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678673	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678677	0.81[ASN][1000 genomes]
rs1678678	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678679	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1678736	0.81[ASN][1000 genomes]
rs1738174	0.85[ASN][1000 genomes]
rs1738175	0.83[ASN][1000 genomes]
rs1738176	0.82[ASN][1000 genomes]
rs1738178	0.82[ASN][1000 genomes]
rs1738179	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1738180	0.81[ASN][1000 genomes]
rs1738181	0.81[ASN][1000 genomes]
rs1738182	0.81[ASN][1000 genomes]
rs1738183	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1738251	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1738252	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738253	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738254	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738255	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738256	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738259	0.86[ASN][1000 genomes]
rs1738260	0.86[ASN][1000 genomes]
rs1738261	0.86[ASN][1000 genomes]
rs1738262	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738264	0.86[ASN][1000 genomes]
rs1738265	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738266	0.86[ASN][1000 genomes]
rs1738267	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738268	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738269	0.85[ASN][1000 genomes]
rs2448400	0.81[ASN][1000 genomes]
rs2448401	0.81[ASN][1000 genomes]
rs4714178	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58817640	0.81[ASN][1000 genomes]
rs9357280	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394532	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38739400-38746600	Weak transcription	K562	blood
2	chr6:38739600-38744600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:38739800-38744200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:38739800-38744200	Weak transcription	HUVEC	blood vessel
5	chr6:38739800-38744400	Weak transcription	HMEC	breast
6	chr6:38741000-38744600	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:38743400-38744400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:38743800-38744200	Enhancers	GM12878-XiMat	blood
9	chr6:38743800-38744800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:38743800-38745000	Enhancers	NHEK	skin
11	chr6:38744000-38744200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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