Variant report

Variant	rs7593440
Chromosome Location	chr2:86550657-86550658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10186289	0.84[CHB][hapmap]
rs10189492	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10200186	0.87[AFR][1000 genomes];0.99[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];0.99[ASN][1000 genomes]
rs10200619	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]
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];0.96[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];0.99[ASN][1000 genomes]
rs11127028	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11127029	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11674249	0.82[AMR][1000 genomes];0.81[ASN][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];1.00[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];0.85[ASN][1000 genomes]
rs12472676	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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];0.99[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];0.99[ASN][1000 genomes]
rs12620833	0.93[CEU][hapmap];0.83[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];0.96[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];0.99[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];0.99[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];0.96[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];0.93[ASN][1000 genomes]
rs13020869	0.82[AFR][1000 genomes];0.99[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];0.96[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];0.99[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];0.97[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];0.98[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];0.81[ASN][1000 genomes]
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];0.99[ASN][1000 genomes]
rs34069316	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35160687	0.81[ASN][1000 genomes]
rs35281683	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35370705	0.85[ASN][1000 genomes]
rs35494267	0.80[AMR][1000 genomes]
rs35762338	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4392258	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.97[ASN][1000 genomes]
rs6714362	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[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];0.97[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];1.00[ASN][1000 genomes]
rs67903513	0.99[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];1.00[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
rs7593440	IMMT	cis	Whole Blood	GTEx
rs7593440	REEP1	cis	multi-tissue	Pritchard
rs7593440	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs7593440	IMMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 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	chr2:86547400-86553200	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:86549200-86563000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:86549800-86551000	Enhancers	Fetal Intestine Small	intestine
12	chr2:86549800-86551600	Enhancers	Fetal Intestine Large	intestine
13	chr2:86550200-86550800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:86550200-86550800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr2:86550200-86554000	Weak transcription	Right Atrium	heart
16	chr2:86550400-86550800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:86550600-86550800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:86550600-86550800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
19	chr2:86550600-86550800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr2:86550600-86550800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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