Variant report

Variant	rs6709005
Chromosome Location	chr2:234828723-234828724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1003540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10166942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10170399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187654	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189040	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs10929309	0.91[JPT][hapmap]
rs10929312	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10929314	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10929319	1.00[YRI][hapmap]
rs11563060	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs11563063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11563066	0.89[ASN][1000 genomes]
rs11563216	0.89[CHB][hapmap];0.89[YRI][hapmap]
rs11563227	0.89[ASN][1000 genomes]
rs11892538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997802	0.89[ASN][1000 genomes]
rs13016127	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13016553	0.89[ASN][1000 genomes]
rs1392606	0.89[ASN][1000 genomes]
rs1965629	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985366	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108809	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs2159200	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2215173	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs2286430	0.86[JPT][hapmap]
rs2302155	0.86[JPT][hapmap]
rs2362290	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2362292	0.83[AFR][1000 genomes]
rs28946911	1.00[YRI][hapmap]
rs4233636	0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4663983	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4663986	0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4663988	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4663990	1.00[YRI][hapmap]
rs6431648	0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6711120	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs6738375	1.00[YRI][hapmap]
rs6738979	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6740118	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs6760630	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs737636	0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7567475	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs758275	0.89[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs758276	0.89[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs758277	0.88[YRI][hapmap]
rs7604471	0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs887061	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs917434	0.86[JPT][hapmap]
rs917435	1.00[YRI][hapmap]
rs968402	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs990418	0.90[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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234826200-234830000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:234827600-234829800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:234827600-234834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:234827800-234833600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:234828400-234829200	Enhancers	HMEC	breast
6	chr2:234828400-234829200	Enhancers	NHEK	skin
7	chr2:234828400-234829400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:234828600-234829000	Enhancers	A549	lung
9	chr2:234828600-234829200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:234828600-234829400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links