Variant report

Variant	rs11903311
Chromosome Location	chr2:99701807-99701808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99701798..99702298-chr2:100170503..100171309,2	K562	blood:
2	chr2:99701627..99702172-chr2:99814711..99815368,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10164941	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10167390	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10170063	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10181422	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1115756	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1115757	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1133977	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1133978	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11683107	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11683188	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11688004	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11692336	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11895749	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12470471	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613624	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12619780	0.92[ASN][1000 genomes]
rs12987548	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13000731	0.85[ASN][1000 genomes]
rs13008171	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13023501	0.84[ASN][1000 genomes]
rs13033012	0.85[ASN][1000 genomes]
rs13407840	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1453563	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1453564	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1563106	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1563107	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1563108	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17708262	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17759607	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2084988	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2516830	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2516833	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2516835	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2632283	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28648058	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34272114	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4346438	0.82[EUR][1000 genomes]
rs4347885	0.83[ASN][1000 genomes]
rs4585080	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4850897	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4851183	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851188	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62154638	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542846	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6542866	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6542868	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6707462	0.82[ASN][1000 genomes]
rs6708878	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6722164	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6724476	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6727749	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6735801	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6737257	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6740054	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6753650	0.92[ASN][1000 genomes]
rs6754843	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720229	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7570657	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7571390	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586608	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7591794	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7599427	0.81[AMR][1000 genomes]
rs7605734	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7606635	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7608938	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11903311	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs11903311	TSGA10	cis	multi-tissue	Pritchard
rs11903311	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11903311	TSGA10	cis	Thyroid	GTEx
rs11903311	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99700400-99707400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99701200-99703000	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links