Variant report

Variant	rs2744658
Chromosome Location	chr1:168732147-168732148
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154960967..154963323-chr1:168731581..168733974,2	MCF-7	breast:
2	chr1:168729436..168732176-chr1:168755143..168757501,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160688	Chromatin interaction
ENSG00000225826	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1018453	0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1052591	0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs12065661	0.81[AFR][1000 genomes]
rs12563398	0.89[ASN][1000 genomes]
rs12567476	0.83[ASN][1000 genomes]
rs12568207	0.89[ASN][1000 genomes]
rs12724380	0.88[ASN][1000 genomes]
rs12728858	0.89[ASN][1000 genomes]
rs12735097	0.83[ASN][1000 genomes]
rs12742262	0.89[ASN][1000 genomes]
rs12748557	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12755391	0.89[ASN][1000 genomes]
rs1555206	1.00[JPT][hapmap]
rs1556790	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1556791	0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs1556792	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1556793	0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs17569416	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1765516	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1765517	0.84[ASN][1000 genomes]
rs1989300	0.89[ASN][1000 genomes]
rs2206288	0.89[ASN][1000 genomes]
rs2206289	0.89[ASN][1000 genomes]
rs2206290	0.89[ASN][1000 genomes]
rs2223478	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744659	0.89[ASN][1000 genomes]
rs2744661	0.89[ASN][1000 genomes]
rs2744665	0.95[ASN][1000 genomes]
rs2786760	0.86[ASN][1000 genomes]
rs2786762	0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2786766	0.82[EUR][1000 genomes]
rs2786767	0.84[EUR][1000 genomes]
rs472668	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs484025	0.89[ASN][1000 genomes]
rs485109	0.89[ASN][1000 genomes]
rs485855	0.89[ASN][1000 genomes]
rs489585	0.89[ASN][1000 genomes]
rs525275	0.86[ASN][1000 genomes]
rs534139	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs538714	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs542198	0.81[CEU][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs555676	0.89[ASN][1000 genomes]
rs609629	0.85[ASN][1000 genomes]
rs610403	0.85[ASN][1000 genomes]
rs623949	0.85[ASN][1000 genomes]
rs625712	0.89[ASN][1000 genomes]
rs627872	0.81[CEU][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6427148	0.81[CEU][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6427149	0.88[ASN][1000 genomes]
rs655128	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs656919	0.89[ASN][1000 genomes]
rs6656646	0.89[ASN][1000 genomes]
rs6666079	0.83[ASN][1000 genomes]
rs6678818	0.83[ASN][1000 genomes]
rs6697889	0.89[ASN][1000 genomes]
rs6701299	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs672950	0.89[ASN][1000 genomes]
rs686610	0.89[ASN][1000 genomes]
rs731949	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs734123	0.89[ASN][1000 genomes]
rs7534485	0.89[ASN][1000 genomes]
rs760912	0.89[ASN][1000 genomes]
rs760913	0.89[ASN][1000 genomes]
rs763433	0.89[ASN][1000 genomes]
rs926431	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv831847	chr1:168669877-168850129	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2744658	FMO9P	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168726200-168736600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:168726400-168735400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:168730000-168735600	Weak transcription	Fetal Heart	heart
4	chr1:168730000-168737200	Weak transcription	Left Ventricle	heart
5	chr1:168730400-168743600	Weak transcription	Psoas Muscle	Psoas
6	chr1:168731400-168733600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:168731400-168733800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:168731600-168732600	Enhancers	HepG2	liver
9	chr1:168731600-168733600	Enhancers	NHEK	skin
10	chr1:168731600-168733800	Enhancers	HMEC	breast
11	chr1:168731800-168733000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links