Variant report

Variant	rs1678669
Chromosome Location	chr6:38756733-38756734
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	chr6:38756306..38758851-chr7:124960777..124963063,2	MCF-7	breast:
2	chr6:38756316..38758833-chr6:38761826..38764671,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1018437	1.00[JPT][hapmap]
rs1157884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614699	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1630487	0.97[ASN][1000 genomes]
rs1678638	1.00[JPT][hapmap]
rs1678657	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1678667	0.92[ASN][1000 genomes]
rs1678675	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678690	0.81[JPT][hapmap]
rs1678717	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1678718	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678725	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678727	0.82[ASN][1000 genomes]
rs1678742	1.00[JPT][hapmap]
rs1738177	0.82[JPT][hapmap]
rs1738184	1.00[JPT][hapmap]
rs1738192	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1738203	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1738220	0.82[JPT][hapmap]
rs1738231	0.83[JPT][hapmap]
rs1738232	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738236	1.00[ASN][1000 genomes]
rs1738238	0.95[ASN][1000 genomes]
rs1738239	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1738240	0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1738241	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1738243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738247	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1738263	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2395709	1.00[JPT][hapmap]
rs2746170	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4286777	1.00[JPT][hapmap]
rs4380739	0.93[JPT][hapmap]
rs4386804	1.00[JPT][hapmap]
rs4391252	1.00[JPT][hapmap]
rs4443498	1.00[JPT][hapmap]
rs4571559	1.00[JPT][hapmap]
rs4590258	1.00[JPT][hapmap]
rs4711558	1.00[JPT][hapmap]
rs4714193	1.00[JPT][hapmap]
rs6458080	1.00[JPT][hapmap]
rs6458081	1.00[JPT][hapmap]
rs6931736	1.00[JPT][hapmap]
rs761348	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769064	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs862422	1.00[JPT][hapmap]
rs862425	1.00[JPT][hapmap]
rs862427	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9296265	1.00[JPT][hapmap]
rs9357290	1.00[JPT][hapmap]
rs9366982	1.00[JPT][hapmap]
rs9369089	1.00[JPT][hapmap]
rs9380789	1.00[JPT][hapmap]
rs9380791	0.87[JPT][hapmap]
rs9380796	1.00[JPT][hapmap]
rs9380798	1.00[JPT][hapmap]
rs9380799	1.00[JPT][hapmap]
rs9394531	0.82[JPT][hapmap]
rs9394547	1.00[JPT][hapmap]
rs9394550	1.00[JPT][hapmap]
rs982705	1.00[JPT][hapmap];0.83[ASN][1000 genomes]

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	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
7	nsv462916	chr6:38747770-38782401	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv602960	chr6:38747770-38782401	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38751800-38763400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:38754600-38764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:38754800-38758200	Enhancers	HUVEC	blood vessel
4	chr6:38755600-38759200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:38756600-38757800	Enhancers	Primary hematopoietic stem cells	blood
6	chr6:38756600-38758200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links