Variant report

Variant	rs552580
Chromosome Location	chr11:121031511-121031512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10892687	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11218155	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11218169	0.98[ASN][1000 genomes]
rs11218175	0.90[ASN][1000 genomes]
rs11218176	0.96[ASN][1000 genomes]
rs11218191	0.95[ASN][1000 genomes]
rs11218198	0.88[ASN][1000 genomes]
rs11524440	0.92[ASN][1000 genomes]
rs12361100	0.82[ASN][1000 genomes]
rs12575628	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1310521	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1310528	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17124937	0.88[ASN][1000 genomes]
rs17124940	0.88[ASN][1000 genomes]
rs17124945	0.87[ASN][1000 genomes]
rs2155364	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2155365	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2155369	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs22298	0.83[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4554895	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs481703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492047	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs492294	0.91[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4935763	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4936580	0.81[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4936593	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs510722	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs527258	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs543119	0.82[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs546916	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs559301	0.81[EUR][1000 genomes]
rs560365	0.85[JPT][hapmap]
rs560401	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs561195	0.85[JPT][hapmap]
rs562281	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576271	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584355	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588917	0.91[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs592160	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs594951	0.82[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs596882	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs599894	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60016568	0.88[ASN][1000 genomes]
rs601102	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs605379	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs618523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs620896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs631969	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs633012	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638463	0.81[EUR][1000 genomes]
rs638496	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs640332	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6589858	0.83[AMR][1000 genomes]
rs662496	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs663031	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677775	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679607	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686882	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs688641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7105435	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs552580	VPS11	cis	cerebellum	SCAN
rs552580	CD3G	cis	cerebellum	SCAN
rs552580	TMEM225	cis	cerebellum	SCAN
rs552580	HINFP	cis	cerebellum	SCAN
rs552580	TAGLN	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120994400-121042400	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:120996800-121037800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:120999600-121041600	Weak transcription	Brain Anterior Caudate	brain
4	chr11:121006400-121035400	Weak transcription	Brain Angular Gyrus	brain
5	chr11:121006400-121040200	Weak transcription	Right Ventricle	heart
6	chr11:121006600-121034800	Weak transcription	HSMMtube	muscle
7	chr11:121008800-121032800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:121009000-121042800	Weak transcription	Pancreas	Pancrea
9	chr11:121011400-121040200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:121017000-121031600	Weak transcription	Gastric	stomach
11	chr11:121017000-121042400	Weak transcription	Brain Substantia Nigra	brain
12	chr11:121020600-121038800	Weak transcription	Ovary	ovary
13	chr11:121024400-121038800	Weak transcription	Left Ventricle	heart
14	chr11:121024400-121041200	Weak transcription	Fetal Brain Female	brain
15	chr11:121025400-121041200	Weak transcription	Psoas Muscle	Psoas
16	chr11:121025600-121041600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:121028800-121039600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:121029000-121032600	Weak transcription	Fetal Stomach	stomach
19	chr11:121029200-121040800	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:121029800-121035800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:121029800-121036200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:121030800-121033800	Weak transcription	Lung	lung
23	chr11:121031000-121031800	Strong transcription	Aorta	Aorta
24	chr11:121031200-121034800	Weak transcription	Fetal Brain Male	brain
25	chr11:121031200-121037600	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links