Variant report

Variant	rs6546839
Chromosome Location	chr2:73680508-73680509
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 167 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10165862	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10169213	0.84[EUR][1000 genomes]
rs10169714	0.84[EUR][1000 genomes]
rs10170786	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.82[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	0.92[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	0.87[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	0.97[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[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[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];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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[CEU][hapmap];1.00[JPT][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	0.97[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];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];1.00[YRI][hapmap];0.90[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]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[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]
rs1881245	1.00[CEU][hapmap];1.00[JPT][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]
rs2056486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[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];0.80[YRI][hapmap];0.84[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.93[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	0.90[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];0.80[YRI][hapmap]
rs6546835	0.83[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[JPT][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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	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]
rs6707722	0.87[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];1.00[YRI][hapmap];1.00[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	0.84[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	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6745368	0.82[EUR][1000 genomes]
rs6745480	0.94[CEU][hapmap];1.00[JPT][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];0.83[EUR][1000 genomes]
rs6756987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[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	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.87[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	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.83[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	0.82[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	0.92[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	0.84[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	0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6546839	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546839	ALMS1P	cis	Whole Blood	GTEx
rs6546839	ALMS1P	cis	Artery Tibial	GTEx
rs6546839	ALMS1	cis	normal skin	skin_eQTL
rs6546839	ALMS1P	cis	Thyroid	GTEx

Chromatin state (count:117 , 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	chr2:73672400-73681200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:73673000-73687200	Weak transcription	NHEK	skin
13	chr2:73673200-73684600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:73673400-73681000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:73673800-73681200	Strong transcription	Fetal Thymus	thymus
16	chr2:73674000-73681000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:73674000-73683800	Strong transcription	Dnd41	blood
18	chr2:73674200-73684200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:73674400-73683000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:73674600-73680800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:73674600-73681200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:73674600-73681200	Strong transcription	Left Ventricle	heart
23	chr2:73674600-73681800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:73674600-73682600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:73674600-73682800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr2:73674600-73682800	Strong transcription	Brain Germinal Matrix	brain
27	chr2:73674600-73683400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:73674600-73685600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:73674800-73680600	Strong transcription	Placenta	Placenta
30	chr2:73675200-73681000	Strong transcription	Primary T cells from cord blood	blood
31	chr2:73675200-73681200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:73675200-73681200	Strong transcription	Fetal Brain Female	brain
33	chr2:73675200-73681200	Strong transcription	HepG2	liver
34	chr2:73675200-73684800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:73675400-73681000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:73675800-73680600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:73675800-73680600	Strong transcription	Fetal Kidney	kidney
38	chr2:73675800-73682800	Strong transcription	Fetal Lung	lung
39	chr2:73675800-73688800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:73676000-73682000	Weak transcription	Liver	Liver
41	chr2:73676200-73682000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:73676200-73684400	Weak transcription	Gastric	stomach
43	chr2:73676200-73719400	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:73676600-73685600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:73676600-73687200	Weak transcription	Esophagus	oesophagus
46	chr2:73676800-73687600	Weak transcription	Brain Substantia Nigra	brain
47	chr2:73676800-73688000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:73676800-73706400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:73677000-73682200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:73677000-73685800	Weak transcription	Rectal Mucosa Donor 31	rectum

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