Variant report

Variant	rs6546838
Chromosome Location	chr2:73679280-73679281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 171 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs10165862	0.81[AMR][1000 genomes]
rs10169213	0.84[EUR][1000 genomes]
rs10169714	0.84[EUR][1000 genomes]
rs10170786	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.82[EUR][1000 genomes]
rs10178678	0.87[EUR][1000 genomes]
rs10179134	0.90[EUR][1000 genomes]
rs10181563	0.80[EUR][1000 genomes]
rs10183818	0.91[EUR][1000 genomes]
rs10184268	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185080	0.84[EUR][1000 genomes]
rs10186501	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.91[EUR][1000 genomes]
rs10187416	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10193972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.84[EUR][1000 genomes]
rs10198549	0.94[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs10199224	0.89[EUR][1000 genomes]
rs10207220	0.84[EUR][1000 genomes]
rs10207264	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469966	0.80[EUR][1000 genomes]
rs10496191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.84[EUR][1000 genomes]
rs11674602	0.91[EUR][1000 genomes]
rs11676385	0.92[EUR][1000 genomes]
rs11679809	0.88[EUR][1000 genomes]
rs11686019	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689588	0.86[EUR][1000 genomes]
rs11693586	0.91[EUR][1000 genomes]
rs11693588	0.91[EUR][1000 genomes]
rs11884776	0.94[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs11899740	0.90[EUR][1000 genomes]
rs11899902	0.91[EUR][1000 genomes]
rs11901272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383871	0.90[EUR][1000 genomes]
rs13384952	0.91[EUR][1000 genomes]
rs13385564	0.89[EUR][1000 genomes]
rs13391258	1.00[ASN][1000 genomes]
rs13391552	0.82[EUR][1000 genomes]
rs13392691	0.90[EUR][1000 genomes]
rs13392872	0.90[EUR][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13400985	0.91[EUR][1000 genomes]
rs13409668	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	0.94[CEU][hapmap]
rs13411311	0.91[EUR][1000 genomes]
rs13421462	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13427832	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428235	0.91[EUR][1000 genomes]
rs13431267	0.82[EUR][1000 genomes]
rs13432605	0.82[EUR][1000 genomes]
rs13538	0.94[CEU][hapmap]
rs1403284	0.92[EUR][1000 genomes]
rs1403412	1.00[YRI][hapmap]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.84[EUR][1000 genomes]
rs17009159	0.84[EUR][1000 genomes]
rs1881244	0.83[AFR][1000 genomes]
rs1881245	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017116	0.89[YRI][hapmap]
rs2056486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.89[EUR][1000 genomes]
rs2421555	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.82[EUR][1000 genomes]
rs2901438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs56014217	0.91[EUR][1000 genomes]
rs56145559	0.86[EUR][1000 genomes]
rs56154726	0.91[EUR][1000 genomes]
rs56672945	0.91[EUR][1000 genomes]
rs58603761	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844734	0.91[EUR][1000 genomes]
rs62151646	0.93[EUR][1000 genomes]
rs62151652	0.93[EUR][1000 genomes]
rs6546827	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs6546835	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.88[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546856	1.00[ASN][1000 genomes]
rs6546857	0.89[CEU][hapmap]
rs6546858	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6705977	1.00[ASN][1000 genomes]
rs6706409	1.00[YRI][hapmap]
rs6707722	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.91[EUR][1000 genomes]
rs6710438	0.81[EUR][1000 genomes]
rs6711001	1.00[ASN][1000 genomes]
rs6711033	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6718843	1.00[ASN][1000 genomes]
rs6719753	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.84[EUR][1000 genomes]
rs6736866	0.95[EUR][1000 genomes]
rs6740223	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.84[EUR][1000 genomes]
rs6741067	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6745368	0.82[EUR][1000 genomes]
rs6745480	0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753344	0.95[EUR][1000 genomes]
rs6755217	0.92[EUR][1000 genomes]
rs6755241	0.92[EUR][1000 genomes]
rs6756885	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6756987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759452	0.82[CEU][hapmap]
rs73947808	0.91[EUR][1000 genomes]
rs7424690	0.83[EUR][1000 genomes]
rs7558944	0.82[EUR][1000 genomes]
rs7564890	0.93[EUR][1000 genomes]
rs7566364	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.91[EUR][1000 genomes]
rs7576245	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs7582606	0.82[EUR][1000 genomes]
rs7583255	0.84[EUR][1000 genomes]
rs7584575	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.84[EUR][1000 genomes]
rs7588169	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7598396	0.95[EUR][1000 genomes]
rs7598419	0.84[EUR][1000 genomes]
rs7598946	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.91[EUR][1000 genomes]
rs7603647	0.82[EUR][1000 genomes]
rs7604682	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.82[EUR][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs9653557	0.84[EUR][1000 genomes]
rs9749859	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.82[EUR][1000 genomes]
rs9753079	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6546838	ALMS1	cis	cerebellum	SCAN
rs6546838	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546838	ALMS1P	cis	Thyroid	GTEx
rs6546838	ALMS1P	cis	Artery Tibial	GTEx
rs6546838	ALMS1P	cis	cerebellum	SCAN
rs6546838	ALMS1P	cis	parietal	SCAN
rs6546838	ALMS1	cis	parietal	SCAN
rs6546838	ALMS1P	cis	Whole Blood	GTEx
rs6546838	ALMS1	cis	normal skin	skin_eQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73645600-73685600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:73647000-73684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:73652200-73688400	Weak transcription	Colonic Mucosa	Colon
4	chr2:73660200-73684400	Weak transcription	HUVEC	blood vessel
5	chr2:73663600-73680600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:73663800-73689400	Weak transcription	NHDF-Ad	bronchial
7	chr2:73664400-73684200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:73664600-73683600	Weak transcription	A549	lung
9	chr2:73665000-73684400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:73665200-73682200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:73667800-73679600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:73672400-73681200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:73673000-73687200	Weak transcription	NHEK	skin
14	chr2:73673200-73684600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:73673400-73681000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:73673800-73679600	Strong transcription	Ovary	ovary
17	chr2:73673800-73681200	Strong transcription	Fetal Thymus	thymus
18	chr2:73674000-73679600	Strong transcription	Adipose Nuclei	Adipose
19	chr2:73674000-73681000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:73674000-73683800	Strong transcription	Dnd41	blood
21	chr2:73674200-73684200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:73674400-73683000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:73674600-73679400	Strong transcription	Fetal Intestine Large	intestine
24	chr2:73674600-73679600	Strong transcription	Thymus	Thymus
25	chr2:73674600-73680000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:73674600-73680800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:73674600-73681200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:73674600-73681200	Strong transcription	Left Ventricle	heart
29	chr2:73674600-73681800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:73674600-73682600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:73674600-73682800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr2:73674600-73682800	Strong transcription	Brain Germinal Matrix	brain
33	chr2:73674600-73683400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:73674600-73685600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:73674800-73680600	Strong transcription	Placenta	Placenta
36	chr2:73675000-73680000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:73675000-73680400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:73675200-73679600	Strong transcription	Lung	lung
39	chr2:73675200-73679800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:73675200-73680000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:73675200-73681000	Strong transcription	Primary T cells from cord blood	blood
42	chr2:73675200-73681200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:73675200-73681200	Strong transcription	Fetal Brain Female	brain
44	chr2:73675200-73681200	Strong transcription	HepG2	liver
45	chr2:73675200-73684800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:73675400-73681000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:73675600-73680200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:73675800-73680600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:73675800-73680600	Strong transcription	Fetal Kidney	kidney
50	chr2:73675800-73682800	Strong transcription	Fetal Lung	lung

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