Variant report

Variant	rs56145559
Chromosome Location	chr2:73623439-73623440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10170849	0.81[EUR][1000 genomes]
rs10178678	0.82[EUR][1000 genomes]
rs10179134	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10183818	0.86[EUR][1000 genomes]
rs10184268	0.91[EUR][1000 genomes]
rs10186501	0.85[EUR][1000 genomes]
rs10187192	0.86[EUR][1000 genomes]
rs10187416	0.82[EUR][1000 genomes]
rs10189574	0.85[EUR][1000 genomes]
rs10190219	0.90[EUR][1000 genomes]
rs10193972	0.84[EUR][1000 genomes]
rs10199224	0.83[EUR][1000 genomes]
rs10207264	0.82[EUR][1000 genomes]
rs10496191	0.86[EUR][1000 genomes]
rs11674602	0.85[EUR][1000 genomes]
rs11676385	0.87[EUR][1000 genomes]
rs11679809	0.93[EUR][1000 genomes]
rs11689392	0.91[EUR][1000 genomes]
rs11689588	0.81[EUR][1000 genomes]
rs11693586	0.85[EUR][1000 genomes]
rs11693588	0.85[EUR][1000 genomes]
rs11884776	0.84[EUR][1000 genomes]
rs11899740	0.95[EUR][1000 genomes]
rs11899902	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13383871	0.95[EUR][1000 genomes]
rs13384952	0.86[EUR][1000 genomes]
rs13385564	0.83[EUR][1000 genomes]
rs13392691	0.85[EUR][1000 genomes]
rs13392872	0.84[EUR][1000 genomes]
rs13398956	0.86[EUR][1000 genomes]
rs13400985	0.86[EUR][1000 genomes]
rs13409668	0.81[EUR][1000 genomes]
rs13411311	0.85[EUR][1000 genomes]
rs13421462	0.86[EUR][1000 genomes]
rs13428235	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1403284	0.87[EUR][1000 genomes]
rs1534471	0.86[EUR][1000 genomes]
rs1881245	0.85[EUR][1000 genomes]
rs1918863	0.87[EUR][1000 genomes]
rs2056486	0.84[EUR][1000 genomes]
rs2140195	0.84[EUR][1000 genomes]
rs2421550	0.87[EUR][1000 genomes]
rs2421552	0.83[EUR][1000 genomes]
rs2901438	0.86[EUR][1000 genomes]
rs3813227	0.86[EUR][1000 genomes]
rs56014217	0.94[EUR][1000 genomes]
rs56154726	0.86[EUR][1000 genomes]
rs56672945	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58603761	0.84[EUR][1000 genomes]
rs60844734	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62151646	0.88[EUR][1000 genomes]
rs62151652	0.88[EUR][1000 genomes]
rs6546835	0.86[EUR][1000 genomes]
rs6546836	0.86[EUR][1000 genomes]
rs6546837	0.86[EUR][1000 genomes]
rs6546838	0.86[EUR][1000 genomes]
rs6546839	0.86[EUR][1000 genomes]
rs6704782	0.80[EUR][1000 genomes]
rs6705489	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6707722	0.86[EUR][1000 genomes]
rs6708766	0.85[EUR][1000 genomes]
rs6719753	0.80[EUR][1000 genomes]
rs6724782	0.86[EUR][1000 genomes]
rs6736866	0.90[EUR][1000 genomes]
rs6740223	0.86[EUR][1000 genomes]
rs6741067	0.85[EUR][1000 genomes]
rs6753344	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6755217	0.92[EUR][1000 genomes]
rs6755241	0.92[EUR][1000 genomes]
rs6756987	0.85[EUR][1000 genomes]
rs73947808	0.86[EUR][1000 genomes]
rs7564890	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7566385	0.81[EUR][1000 genomes]
rs7567585	0.81[EUR][1000 genomes]
rs7572722	0.86[EUR][1000 genomes]
rs7580825	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7584575	0.86[EUR][1000 genomes]
rs7585004	0.86[EUR][1000 genomes]
rs7585124	0.86[EUR][1000 genomes]
rs7588169	0.82[EUR][1000 genomes]
rs7594511	0.90[EUR][1000 genomes]
rs7598396	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7598946	0.86[EUR][1000 genomes]
rs7602980	0.86[EUR][1000 genomes]
rs7607014	0.81[EUR][1000 genomes]
rs9309473	0.85[EUR][1000 genomes]
rs9807961	0.83[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56145559	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs56145559	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs56145559	ALMS1P	cis	Thyroid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73614000-73626200	Weak transcription	Lung	lung
2	chr2:73614200-73626200	Weak transcription	HSMM	muscle
3	chr2:73614400-73626200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:73614400-73626400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:73614400-73626400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:73614600-73641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:73614800-73625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:73614800-73628600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:73615000-73626200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:73615000-73626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:73615000-73626400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:73615000-73626400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:73615000-73626600	Weak transcription	Ovary	ovary
14	chr2:73615000-73628400	Weak transcription	Hela-S3	cervix
15	chr2:73615000-73645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:73615000-73646800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:73615200-73626000	Weak transcription	Primary T cells from cord blood	blood
18	chr2:73615200-73626200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:73615200-73626200	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:73615200-73626200	Weak transcription	Thymus	Thymus
21	chr2:73615200-73646400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:73616000-73626200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:73616200-73625000	Weak transcription	Dnd41	blood
24	chr2:73616400-73626200	Weak transcription	HepG2	liver
25	chr2:73620000-73641200	Weak transcription	Osteobl	bone
26	chr2:73620800-73624800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:73621400-73624200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:73621600-73626600	Weak transcription	Small Intestine	intestine
29	chr2:73621800-73626400	Weak transcription	Fetal Stomach	stomach
30	chr2:73622000-73625000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:73622000-73626200	Weak transcription	Fetal Lung	lung
32	chr2:73622000-73648000	Weak transcription	Fetal Kidney	kidney
33	chr2:73622800-73626200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:73622800-73662800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links