Variant report

Variant	rs2997400
Chromosome Location	chr1:45667440-45667441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45665341..45668545-chr1:45669505..45672315,3	MCF-7	breast:
2	chr1:45658355..45660758-chr1:45665576..45668120,2	MCF-7	breast:
3	chr1:45665675..45667634-chr1:45670275..45673089,2	MCF-7	breast:
4	chr1:45660871..45664355-chr1:45665476..45670240,6	K562	blood:

Variant related genes	Relation type
ENSG00000162415	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11211075	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211077	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211080	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1143726	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1143727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1144866	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1144867	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1144870	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1144871	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1152017	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1152018	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1152020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1152022	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11585488	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11588448	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1226722	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1226723	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1226727	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1226728	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1226736	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226749	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1226911	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1226912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12750360	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16832411	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1698295	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1938302	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1938406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2211644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2356304	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2883902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2997462	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3009973	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3009976	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3009978	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3121731	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3121770	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3128437	0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3128443	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6429558	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6698681	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6700502	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs6702389	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68139854	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7517524	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7528468	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7548075	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7552211	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45660000-45670800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45666400-45668600	Enhancers	HepG2	liver
3	chr1:45666800-45668400	Weak transcription	Brain Germinal Matrix	brain
4	chr1:45666800-45669400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:45667200-45668000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:45667200-45669400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links