Variant report

Variant	rs11899902
Chromosome Location	chr2:73631564-73631565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10169213	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169714	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.85[EUR][1000 genomes]
rs10173534	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178678	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179134	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181563	1.00[ASN][1000 genomes]
rs10183818	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184268	0.96[EUR][1000 genomes]
rs10185080	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186501	0.89[EUR][1000 genomes]
rs10187192	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187416	0.86[EUR][1000 genomes]
rs10189574	0.89[EUR][1000 genomes]
rs10190219	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193972	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs10195357	0.83[EUR][1000 genomes]
rs10195358	0.83[EUR][1000 genomes]
rs10197755	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.94[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199224	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207220	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207264	0.86[EUR][1000 genomes]
rs10469966	1.00[ASN][1000 genomes]
rs10496191	0.91[EUR][1000 genomes]
rs10496192	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs10496193	0.82[EUR][1000 genomes]
rs1052162	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs1114380	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674602	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676385	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679594	1.00[ASN][1000 genomes]
rs11679809	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680965	1.00[ASN][1000 genomes]
rs11686541	1.00[ASN][1000 genomes]
rs11689392	0.95[EUR][1000 genomes]
rs11689588	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693586	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693588	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884776	0.94[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893881	1.00[ASN][1000 genomes]
rs11899740	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901272	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12465867	0.88[ASW][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13383871	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385564	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391552	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392872	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400985	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409366	1.00[ASN][1000 genomes]
rs13409668	0.85[EUR][1000 genomes]
rs13411311	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13421462	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428235	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431267	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432605	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403284	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534471	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1589576	1.00[ASN][1000 genomes]
rs17009149	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009159	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349321	1.00[ASN][1000 genomes]
rs1852647	0.89[YRI][hapmap]
rs1881245	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1918863	0.91[EUR][1000 genomes]
rs2056486	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2140195	0.88[EUR][1000 genomes]
rs2421550	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2421552	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901438	0.91[EUR][1000 genomes]
rs35885918	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3738848	0.84[EUR][1000 genomes]
rs3813227	0.91[EUR][1000 genomes]
rs56014217	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56145559	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56154726	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56672945	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58603761	0.88[EUR][1000 genomes]
rs60844734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149774	1.00[ASN][1000 genomes]
rs62149777	1.00[ASN][1000 genomes]
rs62149781	1.00[ASN][1000 genomes]
rs62149782	1.00[ASN][1000 genomes]
rs62149804	1.00[ASN][1000 genomes]
rs62151564	1.00[ASN][1000 genomes]
rs62151646	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62151652	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153182	1.00[ASN][1000 genomes]
rs62153183	1.00[ASN][1000 genomes]
rs6546827	0.88[CEU][hapmap]
rs6546835	0.91[EUR][1000 genomes]
rs6546836	0.88[CEU][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs6546837	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6546838	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs6546839	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6546845	0.82[EUR][1000 genomes]
rs6546847	0.80[EUR][1000 genomes]
rs6546854	1.00[ASN][1000 genomes]
rs6546857	1.00[ASN][1000 genomes]
rs6704782	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705489	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707722	0.91[EUR][1000 genomes]
rs6708766	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710438	1.00[ASN][1000 genomes]
rs6710659	0.95[YRI][hapmap];0.82[AMR][1000 genomes]
rs6711033	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6719753	0.84[EUR][1000 genomes]
rs6724782	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6735946	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736866	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740223	0.91[EUR][1000 genomes]
rs6740766	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741067	0.90[EUR][1000 genomes]
rs6745368	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747145	0.88[ASW][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6748040	0.88[ASW][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6753344	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755217	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755241	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	0.94[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756987	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs73947808	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424690	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558944	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564890	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.86[EUR][1000 genomes]
rs7567585	0.85[EUR][1000 genomes]
rs7572722	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574291	0.95[YRI][hapmap]
rs7580750	0.80[EUR][1000 genomes]
rs7580825	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582606	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583255	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584575	0.90[EUR][1000 genomes]
rs7585004	0.91[EUR][1000 genomes]
rs7585124	0.91[EUR][1000 genomes]
rs7586463	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587577	1.00[ASN][1000 genomes]
rs7588169	0.86[EUR][1000 genomes]
rs7594511	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596773	1.00[ASN][1000 genomes]
rs7598396	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598419	0.83[EUR][1000 genomes]
rs7598946	0.91[EUR][1000 genomes]
rs7602980	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603647	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604682	0.80[EUR][1000 genomes]
rs7607014	0.86[EUR][1000 genomes]
rs7607892	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs9653557	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.88[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11899902	ALMS1P	cis	cerebellum	SCAN
rs11899902	ALMS1	cis	parietal	SCAN
rs11899902	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11899902	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs11899902	ALMS1P	cis	parietal	SCAN
rs11899902	ALMS1P	cis	Thyroid	GTEx
rs11899902	ALMS1	cis	cerebellum	SCAN
rs11899902	ALMS1P	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

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	chr2:73625200-73637000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:73626600-73653200	Weak transcription	Left Ventricle	heart
10	chr2:73626800-73636800	Weak transcription	Fetal Lung	lung
11	chr2:73626800-73645400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:73626800-73651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:73626800-73651800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:73626800-73662600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:73626800-73662800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:73626800-73662800	Weak transcription	Aorta	Aorta
17	chr2:73626800-73663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:73626800-73664000	Weak transcription	Thymus	Thymus
19	chr2:73627000-73641000	Weak transcription	HSMM	muscle
20	chr2:73627400-73652000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:73627400-73664400	Weak transcription	Pancreas	Pancrea
22	chr2:73627800-73641000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:73628800-73663000	Weak transcription	Hela-S3	cervix
24	chr2:73629000-73632000	ZNF genes & repeats	Dnd41	blood
25	chr2:73629600-73637400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:73630000-73632000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:73630600-73632600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:73630600-73651600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:73631000-73631800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:73631000-73634200	Weak transcription	Esophagus	oesophagus
31	chr2:73631200-73645200	Weak transcription	NHDF-Ad	bronchial
32	chr2:73631400-73631600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:73631400-73632000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr2:73631400-73637400	Weak transcription	Fetal Stomach	stomach
35	chr2:73631400-73642600	Weak transcription	Ovary	ovary
36	chr2:73631400-73652600	Weak transcription	Fetal Intestine Small	intestine
37	chr2:73631400-73659800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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