Variant report

Variant	rs12117066
Chromosome Location	chr1:165495369-165495370
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011469	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1025159	0.85[CEU][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1157861	0.94[EUR][1000 genomes]
rs12126717	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12137629	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs12143824	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs12143868	0.97[ASN][1000 genomes]
rs1326374	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1409413	0.84[EUR][1000 genomes]
rs1425753	0.91[ASN][1000 genomes]
rs16846547	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16846623	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16846756	0.93[EUR][1000 genomes]
rs16847073	0.85[EUR][1000 genomes]
rs2152818	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2252342	0.84[EUR][1000 genomes]
rs2478262	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2553637	0.98[ASN][1000 genomes]
rs2766083	0.94[ASN][1000 genomes]
rs285421	0.91[ASN][1000 genomes]
rs285422	0.88[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs285438	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs285462	1.00[ASN][1000 genomes]
rs285464	0.81[ASN][1000 genomes]
rs285467	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs285468	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs285473	0.98[ASN][1000 genomes]
rs285474	0.98[ASN][1000 genomes]
rs285478	0.98[ASN][1000 genomes]
rs285479	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs285499	0.88[ASN][1000 genomes]
rs285500	0.88[ASN][1000 genomes]
rs401457	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41267552	0.82[EUR][1000 genomes]
rs41267554	0.82[EUR][1000 genomes]
rs56000052	0.88[ASN][1000 genomes]
rs6662135	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669449	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72693816	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72693826	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74120755	0.93[EUR][1000 genomes]
rs7521982	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs7533908	0.93[EUR][1000 genomes]
rs7535829	0.93[EUR][1000 genomes]
rs7535979	0.94[EUR][1000 genomes]
rs7539622	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs927844	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12117066	LRRC52	cis	Stomach	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165493200-165496600	Enhancers	HepG2	liver
2	chr1:165494000-165495400	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr1:165494800-165495400	Flanking Active TSS	Fetal Heart	heart
4	chr1:165494800-165496400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:165495000-165495400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:165495000-165495400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:165495000-165495400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:165495000-165495600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:165495000-165496000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:165495000-165496400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:165495200-165496600	Weak transcription	Fetal Muscle Leg	muscle

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