Variant report

Variant	rs1678666
Chromosome Location	chr6:38754502-38754503
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	chr6:38749592..38751313-chr6:38753149..38755340,2	MCF-7	breast:
2	chr6:38753809..38755972-chr6:38756786..38759773,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1615441	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1616105	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1617807	0.84[EUR][1000 genomes]
rs1618774	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1618834	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1622275	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs1627917	0.84[EUR][1000 genomes]
rs1678639	0.88[YRI][hapmap]
rs1678664	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs1678673	0.83[YRI][hapmap]
rs1678674	0.95[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs1678676	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1678678	0.88[YRI][hapmap]
rs1678686	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs1678710	0.87[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1678711	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678716	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678719	0.87[CEU][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1678720	0.87[CEU][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1678721	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678722	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678724	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678728	0.87[CEU][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1678729	0.87[CEU][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1678730	0.84[EUR][1000 genomes]
rs1678731	0.84[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678732	0.87[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678733	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678734	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678735	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1678737	0.87[CEU][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap]
rs1678738	0.87[CEU][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs1678741	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs1678743	0.82[JPT][hapmap]
rs16891139	0.82[JPT][hapmap]
rs1738179	0.87[YRI][hapmap]
rs1738188	0.82[JPT][hapmap]
rs1738189	0.87[CEU][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs1738190	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs1738191	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1738193	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs1738194	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs1738198	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs1738200	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1738202	0.83[EUR][1000 genomes]
rs1738206	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1738207	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1738208	0.84[EUR][1000 genomes]
rs1738209	0.87[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1738210	0.81[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs1738213	0.84[EUR][1000 genomes]
rs1738214	0.84[EUR][1000 genomes]
rs1738224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1738225	0.81[GIH][hapmap]
rs1738226	0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.88[ASN][1000 genomes]
rs1738227	0.81[GIH][hapmap]
rs1738229	0.81[GIH][hapmap]
rs1738233	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1738234	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1738237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738246	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1738249	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs1738254	0.82[YRI][hapmap]
rs1738262	0.81[YRI][hapmap]
rs1738267	0.83[YRI][hapmap]
rs6912563	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs9470943	0.80[CEU][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1678666	GLP1R	cis	parietal	SCAN
rs1678666	MED20	cis	parietal	SCAN
rs1678666	APOBEC2	cis	parietal	SCAN
rs1678666	ANKS1A	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38751200-38755600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:38751800-38763400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:38753200-38754800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:38754200-38754600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:38754200-38754800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:38754200-38754800	Flanking Active TSS	HUVEC	blood vessel
7	chr6:38754200-38755400	Enhancers	Osteobl	bone
8	chr6:38754400-38754600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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