Variant report

Variant	rs2217888
Chromosome Location	chr14:79877666-79877667
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	chr14:79875683..79878645-chr5:173629859..173632851,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12434126	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12434144	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12435532	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12436125	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12879869	0.84[AMR][1000 genomes]
rs12882679	0.84[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs12884078	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12896672	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12897000	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2167151	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2196442	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196445	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197991	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2370976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370977	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2370978	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2370979	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28889302	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35236866	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35310631	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35441767	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35861800	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36007297	0.82[AMR][1000 genomes]
rs4899743	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4903850	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs4903853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4903856	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61993110	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61993111	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61993112	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61993119	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7150974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv902110	chr14:79624492-79998294	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv530072	chr14:79769657-79928269	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv902111	chr14:79807197-79890677	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2217888	TMED8	cis	cerebellum	SCAN
rs2217888	CAMK1G	trans	parietal	SCAN
rs2217888	ISCA2	cis	cerebellum	SCAN
rs2217888	C14orf169	trans	cerebellum	SCAN
rs2217888	ANGEL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79872600-79884800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:79874200-79877800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr14:79874600-79878200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:79875600-79880000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:79875800-79879800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr14:79875800-79879800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr14:79875800-79880200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr14:79877200-79878600	Enhancers	NHEK	skin
9	chr14:79877400-79878600	Enhancers	HUVEC	blood vessel
10	chr14:79877400-79879600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr14:79877600-79877800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:79877600-79877800	Enhancers	NH-A	brain
13	chr14:79877600-79878400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:79877600-79878400	Enhancers	NHLF	lung
15	chr14:79877600-79878600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links