Variant report

Variant	rs2421545
Chromosome Location	chr2:73639476-73639477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73637836..73639666-chr2:73640939..73642731,2	K562	blood:
2	chr2:73638989..73640908-chr2:73641819..73644176,2	MCF-7	breast:
3	chr2:73612365..73614883-chr2:73639246..73641212,2	K562	blood:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10189578	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10190002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10192125	0.96[ASN][1000 genomes]
rs10519309	0.91[ASN][1000 genomes]
rs1052161	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs1083919	0.87[EUR][1000 genomes]
rs1083921	0.87[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083923	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1091568	0.81[ASN][1000 genomes]
rs11126399	1.00[CHB][hapmap]
rs11126402	0.83[EUR][1000 genomes]
rs11688718	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11890811	0.88[YRI][hapmap]
rs1246094	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1246096	0.82[ASN][1000 genomes]
rs1246105	0.84[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12713783	0.96[ASN][1000 genomes]
rs12995433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12996463	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320374	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs13386124	0.84[EUR][1000 genomes]
rs13399087	0.83[EUR][1000 genomes]
rs1403412	1.00[CHB][hapmap]
rs1406105	0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1528169	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1852645	0.95[ASN][1000 genomes]
rs1852646	0.87[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1881246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1881248	0.91[ASN][1000 genomes]
rs2017116	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2037814	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2091503	0.89[ASN][1000 genomes]
rs2091504	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2140194	0.92[YRI][hapmap]
rs2178154	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421489	0.92[CHB][hapmap]
rs2421546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421548	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421667	0.80[EUR][1000 genomes]
rs2948441	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3820700	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs4852305	0.87[JPT][hapmap]
rs4852306	0.82[ASN][1000 genomes]
rs4852927	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56770679	0.81[ASN][1000 genomes]
rs62153184	0.84[EUR][1000 genomes]
rs6546826	1.00[CHB][hapmap]
rs6546827	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs6546829	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6546830	0.91[ASN][1000 genomes]
rs6546831	0.92[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6546833	0.92[ASN][1000 genomes]
rs6546834	0.96[ASN][1000 genomes]
rs6546842	0.81[ASN][1000 genomes]
rs6706235	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6710659	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6711285	0.89[YRI][hapmap]
rs6722867	0.83[EUR][1000 genomes]
rs6729468	0.84[EUR][1000 genomes]
rs6730785	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732440	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6734450	0.92[ASN][1000 genomes]
rs6743576	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6744697	0.85[EUR][1000 genomes]
rs6745560	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs6746458	0.96[ASN][1000 genomes]
rs6746971	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6749680	0.84[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6757996	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6759464	0.96[ASN][1000 genomes]
rs67898050	0.81[ASN][1000 genomes]
rs68154245	0.82[ASN][1000 genomes]
rs72811907	0.87[ASN][1000 genomes]
rs7562047	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7566315	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7571147	0.92[YRI][hapmap]
rs7574291	1.00[CHB][hapmap]
rs7576824	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7585119	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585663	0.81[YRI][hapmap]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606483	0.85[EUR][1000 genomes]
rs7609249	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs780388	0.83[ASN][1000 genomes]
rs780389	0.83[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs780391	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780393	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780394	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780395	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs802113	0.83[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2421545	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2421545	ALMS1P	cis	Whole Blood	GTEx
rs2421545	TPRKB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73614600-73641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:73615000-73645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:73615000-73646800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:73615200-73646400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:73620000-73641200	Weak transcription	Osteobl	bone
6	chr2:73622000-73648000	Weak transcription	Fetal Kidney	kidney
7	chr2:73622800-73662800	Weak transcription	Right Ventricle	heart
8	chr2:73626600-73653200	Weak transcription	Left Ventricle	heart
9	chr2:73626800-73645400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:73626800-73651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:73626800-73651800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:73626800-73662600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:73626800-73662800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:73626800-73662800	Weak transcription	Aorta	Aorta
15	chr2:73626800-73663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:73626800-73664000	Weak transcription	Thymus	Thymus
17	chr2:73627000-73641000	Weak transcription	HSMM	muscle
18	chr2:73627400-73652000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:73627400-73664400	Weak transcription	Pancreas	Pancrea
20	chr2:73627800-73641000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:73628800-73663000	Weak transcription	Hela-S3	cervix
22	chr2:73630600-73651600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:73631200-73645200	Weak transcription	NHDF-Ad	bronchial
24	chr2:73631400-73642600	Weak transcription	Ovary	ovary
25	chr2:73631400-73652600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:73631400-73659800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:73631800-73645400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:73632000-73646200	Weak transcription	Dnd41	blood
29	chr2:73632000-73651800	Weak transcription	HepG2	liver
30	chr2:73632400-73646400	Weak transcription	Primary B cells from cord blood	blood
31	chr2:73632400-73651800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:73632400-73658800	Weak transcription	Liver	Liver
33	chr2:73632600-73645400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:73633200-73650800	Weak transcription	Fetal Thymus	thymus
35	chr2:73633200-73662800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:73633600-73646600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:73633800-73651000	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:73634000-73659200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:73634000-73661400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:73634000-73663200	Weak transcription	Psoas Muscle	Psoas
41	chr2:73634200-73652200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:73634400-73662000	Weak transcription	Lung	lung
43	chr2:73634400-73662800	Weak transcription	Esophagus	oesophagus
44	chr2:73634600-73645800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:73634600-73661800	Weak transcription	Brain Germinal Matrix	brain
46	chr2:73634800-73645400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:73634800-73652600	Weak transcription	Fetal Intestine Large	intestine
48	chr2:73634800-73659600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:73635000-73646200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:73635000-73647800	Weak transcription	Fetal Muscle Trunk	muscle

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