Variant report

Variant	rs2898260
Chromosome Location	chr8:10939490-10939491
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10099881	0.84[ASN][1000 genomes]
rs10105315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10108304	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10108618	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs10113735	0.84[ASN][1000 genomes]
rs10113808	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11773990	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777887	1.00[CHB][hapmap]
rs11777918	1.00[CHB][hapmap]
rs11778398	1.00[CHB][hapmap]
rs11986748	1.00[JPT][hapmap]
rs11991118	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11991121	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11991716	1.00[CHB][hapmap]
rs12542383	0.84[ASN][1000 genomes]
rs17723229	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17724226	1.00[CHB][hapmap]
rs17724467	0.93[CEU][hapmap]
rs17780806	1.00[CHB][hapmap]
rs2001329	0.81[CEU][hapmap]
rs2001433	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2409685	0.80[CEU][hapmap]
rs2409689	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2409691	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2409692	1.00[CHB][hapmap]
rs2409694	1.00[CHB][hapmap]
rs2409710	0.86[CEU][hapmap]
rs2409720	1.00[CHB][hapmap]
rs28510951	0.84[ASN][1000 genomes]
rs28722721	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2898256	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898257	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898258	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3021494	0.85[CEU][hapmap]
rs3021500	0.82[CEU][hapmap]
rs34094119	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4262293	0.84[ASN][1000 genomes]
rs4333549	0.85[CEU][hapmap]
rs4523214	0.93[CEU][hapmap]
rs4840542	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs4840551	1.00[CHB][hapmap]
rs4841489	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841490	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4841495	0.93[CEU][hapmap]
rs55676920	0.84[ASN][1000 genomes]
rs55813668	0.84[ASN][1000 genomes]
rs59724806	0.84[ASN][1000 genomes]
rs60134032	0.84[ASN][1000 genomes]
rs6601559	0.83[AMR][1000 genomes]
rs6601560	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs6601561	0.80[CEU][hapmap]
rs6601562	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6601564	0.85[CEU][hapmap]
rs66475020	0.84[ASN][1000 genomes]
rs6980856	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982381	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6991930	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs6999969	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7011756	0.82[CEU][hapmap]
rs7014291	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7017567	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463505	0.84[ASN][1000 genomes]
rs7820860	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes]
rs7825690	1.00[CHB][hapmap]
rs7835318	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs9329235	0.84[ASN][1000 genomes]
rs9657519	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2898260	AF131215.9	cis	Skin Sun Exposed Lower leg	GTEx
rs2898260	AF131215.2	cis	Nerve Tibial	GTEx
rs2898260	C8orf5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10925000-10941800	Weak transcription	Right Atrium	heart
2	chr8:10925600-10944400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:10932000-10939800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr8:10935200-10943800	Weak transcription	Brain Anterior Caudate	brain
5	chr8:10935600-10939800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr8:10936600-10940600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:10937800-10940000	Enhancers	HMEC	breast
8	chr8:10937800-10941000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr8:10938000-10940200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:10938600-10939600	Flanking Active TSS	NHEK	skin
11	chr8:10939000-10939600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:10939200-10939600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr8:10939200-10939600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:10939400-10939600	Enhancers	Pancreas	Pancrea
15	chr8:10939400-10939800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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