Variant report

Variant	rs17155393
Chromosome Location	chr8:9981637-9981638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10107485	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs11249969	0.81[JPT][hapmap]
rs1160369	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11774411	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11783851	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11785434	0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11785454	0.85[ASN][1000 genomes]
rs11990610	0.82[CHB][hapmap]
rs11990614	0.82[CHB][hapmap]
rs12542030	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs12545469	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12545775	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12545788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12545826	0.81[JPT][hapmap]
rs12547884	0.83[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12549943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550244	0.86[CHB][hapmap]
rs12674871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12679328	0.85[JPT][hapmap]
rs12680389	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13249013	0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13256357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1466555	0.84[ASN][1000 genomes]
rs1484645	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1564808	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs17151140	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs17151142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17151145	0.83[CHB][hapmap]
rs17151147	0.83[CHB][hapmap]
rs17151190	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17151201	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1984863	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2016221	0.88[ASN][1000 genomes]
rs2409632	0.81[JPT][hapmap]
rs2898242	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs3735823	0.81[JPT][hapmap]
rs4294187	0.86[CHB][hapmap]
rs4840462	0.81[JPT][hapmap]
rs4840463	0.82[CHB][hapmap]
rs4841279	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4841283	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66602888	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6983566	0.81[JPT][hapmap]
rs6985791	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6997865	0.81[JPT][hapmap]
rs7008407	0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7008695	0.82[ASN][1000 genomes]
rs7012601	0.87[ASN][1000 genomes]
rs7016690	0.87[ASN][1000 genomes]
rs72626643	0.81[ASN][1000 genomes]
rs7830843	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9329215	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs9644681	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17155393	LONRF1	cis	parietal	SCAN
rs17155393	FLJ10661	cis	cerebellum	SCAN
rs17155393	CLDN23	cis	multi-tissue	Pritchard
rs17155393	C8orf48	cis	cerebellum	SCAN
rs17155393	RBPMS	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9970600-9995800	Weak transcription	Pancreas	Pancrea
2	chr8:9975600-9987400	Weak transcription	Brain Germinal Matrix	brain
3	chr8:9977000-9988000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr8:9978200-9988000	Weak transcription	Fetal Brain Female	brain
5	chr8:9980600-9988200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:9981200-9982000	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links