Variant report

Variant	rs230853
Chromosome Location	chr5:56959619-56959620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10057570	0.93[AFR][1000 genomes]
rs10057880	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10069403	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10077005	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10487613	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487614	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10940569	0.84[EUR][1000 genomes]
rs10940570	0.83[EUR][1000 genomes]
rs11738377	0.84[EUR][1000 genomes]
rs11738862	0.84[EUR][1000 genomes]
rs11740506	0.84[EUR][1000 genomes]
rs11742166	0.84[EUR][1000 genomes]
rs12153161	0.84[EUR][1000 genomes]
rs12520986	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12652614	0.84[EUR][1000 genomes]
rs13161204	0.84[EUR][1000 genomes]
rs13177900	0.83[EUR][1000 genomes]
rs13185580	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1347071	1.00[YRI][hapmap]
rs1476831	0.84[EUR][1000 genomes]
rs1476832	0.84[EUR][1000 genomes]
rs170740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170741	0.93[AFR][1000 genomes]
rs1821210	1.00[YRI][hapmap]
rs183477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861052	0.81[AFR][1000 genomes]
rs1861059	1.00[YRI][hapmap]
rs2017201	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2041678	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2161500	0.81[AFR][1000 genomes]
rs2191445	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2191446	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2191448	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2191449	0.84[EUR][1000 genomes]
rs2215420	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215421	0.82[EUR][1000 genomes]
rs229960	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs229961	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs229963	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs229965	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs230823	0.85[EUR][1000 genomes]
rs230824	0.84[EUR][1000 genomes]
rs230825	0.84[EUR][1000 genomes]
rs230826	0.84[EUR][1000 genomes]
rs230827	0.83[EUR][1000 genomes]
rs230846	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230847	0.85[EUR][1000 genomes]
rs230848	0.85[EUR][1000 genomes]
rs230849	0.85[EUR][1000 genomes]
rs230850	0.85[EUR][1000 genomes]
rs230851	0.85[EUR][1000 genomes]
rs230852	0.85[EUR][1000 genomes]
rs230854	0.84[EUR][1000 genomes]
rs230855	0.84[EUR][1000 genomes]
rs230856	0.84[EUR][1000 genomes]
rs230857	0.84[EUR][1000 genomes]
rs230858	0.84[EUR][1000 genomes]
rs230859	0.84[EUR][1000 genomes]
rs230860	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230861	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2408846	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2408849	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2408850	0.86[AFR][1000 genomes]
rs2408854	1.00[YRI][hapmap]
rs2568537	1.00[YRI][hapmap]
rs2898028	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4141128	0.83[EUR][1000 genomes]
rs4235474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508990	0.86[AFR][1000 genomes]
rs4699909	0.84[EUR][1000 genomes]
rs4699910	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4699913	1.00[YRI][hapmap]
rs4700210	0.84[EUR][1000 genomes]
rs4700211	0.84[EUR][1000 genomes]
rs4700214	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4700233	1.00[YRI][hapmap]
rs6450430	0.96[EUR][1000 genomes]
rs6450431	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6866242	0.86[AFR][1000 genomes]
rs6886241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702695	0.85[EUR][1000 genomes]
rs702696	0.85[EUR][1000 genomes]
rs7714534	0.84[EUR][1000 genomes]
rs7719947	0.84[EUR][1000 genomes]
rs7726732	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732108	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7737409	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs854036	1.00[YRI][hapmap]
rs854137	0.85[EUR][1000 genomes]
rs887503	0.84[EUR][1000 genomes]
rs917655	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986101	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs991727	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][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	nsv830309	chr5:56837590-56978283	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56946800-56961200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:56955200-56960600	Weak transcription	Liver	Liver
3	chr5:56957400-56964200	Enhancers	Fetal Heart	heart
4	chr5:56958200-56960000	Enhancers	Left Ventricle	heart
5	chr5:56958800-56960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:56958800-56960800	Weak transcription	Pancreas	Pancrea
7	chr5:56959200-56960800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:56959400-56960000	Enhancers	Right Atrium	heart
9	chr5:56959400-56960600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:56959400-56961400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:56959400-56961800	Weak transcription	Right Ventricle	heart
12	chr5:56959600-56961800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links