Variant report

Variant	rs10200619
Chromosome Location	chr2:86548848-86548849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10186289	0.84[CHB][hapmap]
rs10189492	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10200186	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10200526	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10201457	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10520415	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11127026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11127028	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11127029	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11674249	0.82[AMR][1000 genomes]
rs11675942	0.85[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs11681689	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs11685863	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691122	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11691726	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap]
rs11691807	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12052607	0.86[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs12466728	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs12472390	0.93[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs12472676	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12476706	0.86[CEU][hapmap]
rs12476826	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs12478575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12478653	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12620833	0.93[CEU][hapmap];0.81[ASN][1000 genomes]
rs12622200	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12714179	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12714180	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12988844	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12999029	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs13015186	0.86[CEU][hapmap]
rs13017143	0.81[CEU][hapmap]
rs13017338	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13020869	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13023154	0.85[CEU][hapmap]
rs13024964	0.89[CEU][hapmap]
rs13421310	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17438687	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs17737955	0.86[CEU][hapmap]
rs17738096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1863051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863059	0.85[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs1863063	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs2278105	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2303359	0.82[AMR][1000 genomes]
rs2367233	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34048420	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34069316	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35281683	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs35370705	0.84[ASN][1000 genomes]
rs35494267	0.80[AMR][1000 genomes]
rs35762338	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4392258	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832031	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4832033	0.82[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs4832261	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4832262	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs4832269	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4832270	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs6547668	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs6547673	0.84[CHB][hapmap]
rs6547674	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713456	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6714362	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6725234	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs6728029	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738585	0.81[AMR][1000 genomes]
rs67407963	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6745235	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs6746198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67903513	0.97[ASN][1000 genomes]
rs7560886	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs7563887	0.84[CHB][hapmap]
rs7571424	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7593440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9677502	0.81[CEU][hapmap];0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10200619	REEP1	cis	multi-tissue	Pritchard
rs10200619	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs10200619	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs10200619	IMMT	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86533200-86563000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:86536200-86559800	Weak transcription	HSMMtube	muscle
3	chr2:86537600-86563000	Weak transcription	Brain Anterior Caudate	brain
4	chr2:86539400-86552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:86541400-86551600	Weak transcription	Fetal Brain Female	brain
6	chr2:86542200-86559400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:86543000-86556800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:86546800-86555000	Weak transcription	Left Ventricle	heart
9	chr2:86547000-86549800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:86547400-86553200	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:86548200-86549800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:86548600-86549800	Weak transcription	Fetal Intestine Large	intestine
13	chr2:86548600-86550000	Weak transcription	Right Atrium	heart

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