Variant report

Variant	rs6546854
Chromosome Location	chr2:73834034-73834035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 175 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10168931	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169213	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169714	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170786	0.91[EUR][1000 genomes]
rs10170849	0.83[EUR][1000 genomes]
rs10173534	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178409	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10178678	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179134	1.00[ASN][1000 genomes]
rs10181563	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183818	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185080	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186501	0.80[EUR][1000 genomes]
rs10187192	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187416	0.82[EUR][1000 genomes]
rs10189574	0.80[EUR][1000 genomes]
rs10190219	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193972	0.82[EUR][1000 genomes]
rs10197409	0.90[EUR][1000 genomes]
rs10197755	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199224	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206899	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10207220	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207264	0.82[EUR][1000 genomes]
rs10209517	0.94[EUR][1000 genomes]
rs10469966	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496192	1.00[ASN][1000 genomes]
rs10496193	0.87[EUR][1000 genomes]
rs1052162	0.95[EUR][1000 genomes]
rs11126404	0.83[EUR][1000 genomes]
rs1114380	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674602	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675958	1.00[ASN][1000 genomes]
rs11676385	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679594	1.00[ASN][1000 genomes]
rs11679809	1.00[ASN][1000 genomes]
rs11680965	1.00[ASN][1000 genomes]
rs11686019	0.84[EUR][1000 genomes]
rs11686541	1.00[ASN][1000 genomes]
rs11689164	1.00[ASN][1000 genomes]
rs11689588	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693586	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693588	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884776	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893881	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899740	1.00[ASN][1000 genomes]
rs11899902	1.00[ASN][1000 genomes]
rs11903916	0.91[EUR][1000 genomes]
rs13383871	1.00[ASN][1000 genomes]
rs13384756	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385564	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391258	0.85[EUR][1000 genomes]
rs13391552	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392872	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398956	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400985	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409366	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409668	0.83[EUR][1000 genomes]
rs13410232	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411311	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13421462	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427832	0.94[EUR][1000 genomes]
rs13428235	1.00[ASN][1000 genomes]
rs13431267	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431529	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432605	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13538	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403284	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589576	1.00[ASN][1000 genomes]
rs17009149	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009159	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349321	1.00[ASN][1000 genomes]
rs2056486	0.82[EUR][1000 genomes]
rs2140195	0.81[EUR][1000 genomes]
rs2421552	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421555	0.91[EUR][1000 genomes]
rs2421577	0.94[EUR][1000 genomes]
rs2567598	1.00[ASN][1000 genomes]
rs2567601	1.00[ASN][1000 genomes]
rs2567602	1.00[ASN][1000 genomes]
rs2567603	1.00[ASN][1000 genomes]
rs28879089	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.82[EUR][1000 genomes]
rs4547554	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56014217	1.00[ASN][1000 genomes]
rs56154726	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56672945	1.00[ASN][1000 genomes]
rs58603761	0.82[EUR][1000 genomes]
rs60844734	1.00[ASN][1000 genomes]
rs62149774	1.00[ASN][1000 genomes]
rs62149777	1.00[ASN][1000 genomes]
rs62149781	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62151652	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153182	1.00[ASN][1000 genomes]
rs62153183	1.00[ASN][1000 genomes]
rs6546845	0.87[EUR][1000 genomes]
rs6546847	0.89[EUR][1000 genomes]
rs6546849	0.94[EUR][1000 genomes]
rs6546850	0.95[EUR][1000 genomes]
rs6546851	0.95[EUR][1000 genomes]
rs6546852	0.95[EUR][1000 genomes]
rs6546853	0.95[EUR][1000 genomes]
rs6546856	0.91[EUR][1000 genomes]
rs6546857	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546858	0.94[EUR][1000 genomes]
rs6546859	0.94[EUR][1000 genomes]
rs6546860	0.94[EUR][1000 genomes]
rs6546861	0.85[EUR][1000 genomes]
rs6704782	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705489	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705977	0.85[EUR][1000 genomes]
rs6708766	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710438	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711001	0.86[EUR][1000 genomes]
rs6711033	0.82[EUR][1000 genomes]
rs6718843	0.85[EUR][1000 genomes]
rs6719753	0.81[EUR][1000 genomes]
rs6723247	0.94[EUR][1000 genomes]
rs6726694	0.94[EUR][1000 genomes]
rs6735946	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736866	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744398	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745368	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745480	0.94[EUR][1000 genomes]
rs6753344	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755217	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755241	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756987	0.80[EUR][1000 genomes]
rs6759452	1.00[ASN][1000 genomes]
rs73947808	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424690	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558944	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564890	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566364	0.94[EUR][1000 genomes]
rs7566385	0.82[EUR][1000 genomes]
rs7567585	0.82[EUR][1000 genomes]
rs7572722	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576245	0.95[EUR][1000 genomes]
rs7580750	0.89[EUR][1000 genomes]
rs7580825	1.00[ASN][1000 genomes]
rs7582051	1.00[ASN][1000 genomes]
rs7582606	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583255	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587577	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588169	0.82[EUR][1000 genomes]
rs7594511	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596773	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598396	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598419	0.94[EUR][1000 genomes]
rs7602980	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603647	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604682	0.89[EUR][1000 genomes]
rs7607014	0.82[EUR][1000 genomes]
rs7607892	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9653557	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749859	0.91[EUR][1000 genomes]
rs9750915	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv961795	chr2:73830604-73834098	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6546854	ALMS1P	cis	Nerve Tibial	GTEx
rs6546854	ALMS1P	cis	Thyroid	GTEx
rs6546854	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6546854	ALMS1P	cis	Whole Blood	GTEx
rs6546854	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
2	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
3	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
4	chr2:73815600-73836000	Weak transcription	A549	lung
5	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
6	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:73827000-73840600	Weak transcription	NHLF	lung
13	chr2:73827200-73837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:73827400-73836400	Strong transcription	Primary T cells from cord blood	blood
15	chr2:73827600-73837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:73827600-73838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:73828800-73837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:73829000-73837600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:73829000-73839000	Weak transcription	NHDF-Ad	bronchial
22	chr2:73829000-73839400	Weak transcription	Placenta	Placenta
23	chr2:73829200-73838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:73829200-73840000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:73829600-73835600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:73829600-73837200	Weak transcription	Lung	lung
28	chr2:73829600-73837600	Weak transcription	Pancreas	Pancrea
29	chr2:73829600-73840200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:73829800-73835400	Weak transcription	Right Ventricle	heart
31	chr2:73829800-73838000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:73829800-73839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:73829800-73840000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:73829800-73840000	Weak transcription	Gastric	stomach
35	chr2:73829800-73840400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:73830000-73840800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:73830200-73838000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:73830400-73835400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:73830400-73835600	Weak transcription	Brain Anterior Caudate	brain
40	chr2:73830400-73835800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:73830400-73839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:73830400-73843600	Weak transcription	Aorta	Aorta
43	chr2:73830600-73835400	Weak transcription	Fetal Thymus	thymus
44	chr2:73830600-73835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:73830600-73835600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:73830600-73835600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:73830600-73835600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:73830600-73835600	Weak transcription	HSMM	muscle
49	chr2:73830600-73835800	Weak transcription	Brain Germinal Matrix	brain
50	chr2:73830600-73836200	Weak transcription	NH-A	brain

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