Variant report

Variant	rs12153887
Chromosome Location	chr2:229942755-229942756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10806337	0.82[EUR][1000 genomes]
rs10944136	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10944137	0.81[EUR][1000 genomes]
rs10944138	0.85[EUR][1000 genomes]
rs10944144	0.99[EUR][1000 genomes]
rs10944145	0.99[EUR][1000 genomes]
rs10944147	0.95[EUR][1000 genomes]
rs10944151	0.93[EUR][1000 genomes]
rs10944152	0.94[EUR][1000 genomes]
rs10944157	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11752180	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11752223	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11754330	0.81[EUR][1000 genomes]
rs11755642	0.81[EUR][1000 genomes]
rs11758508	0.89[EUR][1000 genomes]
rs12190603	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12191212	0.94[EUR][1000 genomes]
rs12192546	0.82[EUR][1000 genomes]
rs12193904	0.81[EUR][1000 genomes]
rs12196377	0.92[EUR][1000 genomes]
rs12198061	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12198557	0.93[EUR][1000 genomes]
rs12198730	0.94[EUR][1000 genomes]
rs12199329	0.99[EUR][1000 genomes]
rs12202712	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205492	0.81[EUR][1000 genomes]
rs12209668	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12211216	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12212480	0.81[EUR][1000 genomes]
rs12215159	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12660846	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12665464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12665516	0.99[EUR][1000 genomes]
rs12665542	0.99[EUR][1000 genomes]
rs13201730	0.95[EUR][1000 genomes]
rs13203309	0.98[EUR][1000 genomes]
rs13203560	0.97[EUR][1000 genomes]
rs13207173	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13207537	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13209671	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13209740	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13213603	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13214489	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13219504	0.95[EUR][1000 genomes]
rs1335442	0.80[EUR][1000 genomes]
rs1447160	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470531	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1813001	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1838954	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1838955	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1838958	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1838959	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084293	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084294	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084296	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084297	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2100109	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2121594	0.89[EUR][1000 genomes]
rs2166665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2197648	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2218594	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2225754	0.81[EUR][1000 genomes]
rs2324817	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34622605	0.81[EUR][1000 genomes]
rs34765423	0.85[EUR][1000 genomes]
rs34795473	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35874630	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36035797	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36053156	0.91[EUR][1000 genomes]
rs4098044	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4706246	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4706247	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4706248	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706252	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4706253	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707223	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707229	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707236	0.82[ASN][1000 genomes]
rs57016132	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61119084	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454487	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454488	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66807489	0.83[ASN][1000 genomes]
rs67024565	0.95[EUR][1000 genomes]
rs6900436	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739241	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755730	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9647601	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12153887	SNHG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:229929000-229948400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:229931600-229945000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:229932000-229952800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:229932400-229944600	Weak transcription	Aorta	Aorta
5	chr2:229933400-229952000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:229936200-229946200	Weak transcription	HSMMtube	muscle
7	chr2:229936600-229947000	Weak transcription	HSMM	muscle
8	chr2:229940600-229952000	Weak transcription	Ovary	ovary
9	chr2:229940800-229947000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:229940800-229953200	Weak transcription	Fetal Lung	lung
11	chr2:229941000-229942800	Weak transcription	Liver	Liver
12	chr2:229941000-229951400	Weak transcription	Left Ventricle	heart
13	chr2:229942200-229948000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:229942600-229943600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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