Variant report

Variant	rs6601560
Chromosome Location	chr8:10950866-10950867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10096421	0.83[CEU][hapmap]
rs10105315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10106207	0.87[CEU][hapmap]
rs10108618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113808	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes]
rs10156356	1.00[CHB][hapmap]
rs1057626	0.83[AMR][1000 genomes]
rs11250099	0.87[CEU][hapmap]
rs11773990	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11777887	1.00[CHB][hapmap]
rs11777918	1.00[CHB][hapmap]
rs11778398	1.00[CHB][hapmap]
rs11991118	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs11991716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17723229	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17724226	1.00[CHB][hapmap]
rs17724467	0.92[CEU][hapmap]
rs17780806	1.00[CHB][hapmap]
rs2001329	0.81[CEU][hapmap]
rs2001433	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2409685	0.80[CEU][hapmap]
rs2409689	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2409691	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2409692	1.00[CHB][hapmap]
rs2409694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2409698	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2409701	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2409710	0.83[CEU][hapmap]
rs2409718	0.86[CEU][hapmap]
rs2409720	1.00[CHB][hapmap]
rs2409722	0.82[CEU][hapmap]
rs28719598	0.85[ASN][1000 genomes]
rs28722721	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898256	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2898257	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2898260	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs3021494	0.82[CEU][hapmap]
rs3021500	0.87[CEU][hapmap]
rs34094119	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4333549	0.83[CEU][hapmap]
rs4523214	0.91[CEU][hapmap]
rs4840542	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840544	0.83[AMR][1000 genomes]
rs4840551	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs4841465	0.83[CEU][hapmap]
rs4841489	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4841490	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4841495	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4841498	0.82[CEU][hapmap]
rs4841504	0.82[CEU][hapmap]
rs6601559	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601561	0.84[CEU][hapmap]
rs6601562	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs6601564	0.82[CEU][hapmap]
rs6980856	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6982381	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991930	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs7011756	0.87[CEU][hapmap]
rs7017567	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7812573	0.85[ASN][1000 genomes]
rs7813802	0.82[CEU][hapmap]
rs7819412	0.82[CEU][hapmap]
rs7820860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825690	1.00[CHB][hapmap]
rs7835318	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657519	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3352540	chr8:10950725-10951225	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv3361935	chr8:10950745-10951195	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6601560	AF131215.9	cis	Skin Sun Exposed Lower leg	GTEx
rs6601560	C8orf5	cis	uninvolved skin	skin_eQTL
rs6601560	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs6601560	C8orf5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10949200-10951000	Enhancers	Stomach Mucosa	stomach
2	chr8:10950000-10955400	Weak transcription	Fetal Heart	heart
3	chr8:10950400-10951000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:10950600-10951000	Enhancers	Duodenum Mucosa	Duodenum
5	chr8:10950600-10954000	Weak transcription	Pancreas	Pancrea
6	chr8:10950600-10965000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links