Variant report

Variant	rs1052162
Chromosome Location	chr2:73829372-73829373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:73829123-73829404	IMR90	lung:	n/a	chr2:73829259-73829270 chr2:73829259-73829272

Variant related genes	Relation type
ALMS1	TF binding region

Extended variants
information (count: 159 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10169213	0.89[EUR][1000 genomes]
rs10169714	0.90[EUR][1000 genomes]
rs10170786	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.91[EUR][1000 genomes]
rs10178409	0.87[EUR][1000 genomes]
rs10178678	0.84[EUR][1000 genomes]
rs10181563	0.85[EUR][1000 genomes]
rs10183818	0.81[EUR][1000 genomes]
rs10184268	1.00[ASN][1000 genomes]
rs10185080	0.89[EUR][1000 genomes]
rs10186501	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.81[EUR][1000 genomes]
rs10187416	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	1.00[CEU][hapmap]
rs10193972	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.89[EUR][1000 genomes]
rs10198549	0.94[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs10199224	0.82[EUR][1000 genomes]
rs10206899	0.94[CEU][hapmap]
rs10207220	0.89[EUR][1000 genomes]
rs10207264	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496191	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.89[EUR][1000 genomes]
rs11674602	0.82[EUR][1000 genomes]
rs11676385	0.82[EUR][1000 genomes]
rs11686019	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	1.00[ASN][1000 genomes]
rs11689588	0.87[EUR][1000 genomes]
rs11693586	0.82[EUR][1000 genomes]
rs11693588	0.82[EUR][1000 genomes]
rs11884776	0.94[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11893881	0.94[EUR][1000 genomes]
rs11901272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.82[EUR][1000 genomes]
rs13385564	0.81[EUR][1000 genomes]
rs13391258	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391552	0.91[EUR][1000 genomes]
rs13392691	0.82[EUR][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13400985	0.81[EUR][1000 genomes]
rs13409366	0.94[EUR][1000 genomes]
rs13409668	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	0.94[CEU][hapmap]
rs13411311	0.82[EUR][1000 genomes]
rs13421462	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13427832	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431267	0.86[EUR][1000 genomes]
rs13432605	0.91[EUR][1000 genomes]
rs13538	0.94[CEU][hapmap]
rs1403284	0.82[EUR][1000 genomes]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.89[EUR][1000 genomes]
rs17009159	0.89[EUR][1000 genomes]
rs1881245	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056486	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.82[EUR][1000 genomes]
rs2421555	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.91[EUR][1000 genomes]
rs2901438	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs56154726	0.82[EUR][1000 genomes]
rs58603761	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149781	0.88[EUR][1000 genomes]
rs62151646	0.80[EUR][1000 genomes]
rs62151652	0.80[EUR][1000 genomes]
rs6546835	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	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]
rs6546839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546854	0.95[EUR][1000 genomes]
rs6546856	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs6546858	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	1.00[CEU][hapmap]
rs6705977	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707722	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.82[EUR][1000 genomes]
rs6710438	0.91[EUR][1000 genomes]
rs6711001	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711033	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6718843	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719753	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.89[EUR][1000 genomes]
rs6740223	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.89[EUR][1000 genomes]
rs6745368	0.91[EUR][1000 genomes]
rs6745480	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	0.94[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs6756987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759452	0.82[CEU][hapmap]
rs73947808	0.82[EUR][1000 genomes]
rs7424690	0.88[EUR][1000 genomes]
rs7558944	0.91[EUR][1000 genomes]
rs7566364	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.82[EUR][1000 genomes]
rs7576245	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs7582606	0.91[EUR][1000 genomes]
rs7583255	0.89[EUR][1000 genomes]
rs7584575	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.89[EUR][1000 genomes]
rs7587577	0.95[EUR][1000 genomes]
rs7588169	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	1.00[CEU][hapmap]
rs7596773	0.94[EUR][1000 genomes]
rs7598419	0.89[EUR][1000 genomes]
rs7598946	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.81[EUR][1000 genomes]
rs7603647	0.91[EUR][1000 genomes]
rs7604682	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.91[EUR][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs9653557	0.89[EUR][1000 genomes]
rs9749859	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.91[EUR][1000 genomes]
rs9753079	1.00[ASN][1000 genomes]
rs9807961	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1052162	ALMS1	cis	normal skin	skin_eQTL
rs1052162	ALMS1	cis	multi-tissue	Pritchard
rs1052162	ALMS1	cis	parietal	SCAN
rs1052162	ALMS1P	cis	cerebellum	SCAN
rs1052162	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs1052162	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1052162	ALMS1P	cis	Thyroid	GTEx
rs1052162	ALMS1	cis	cerebellum	SCAN
rs1052162	ALMS1P	cis	parietal	SCAN
rs1052162	ALMS1P	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

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	chr2:73819600-73829400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:73821600-73830000	Weak transcription	Osteobl	bone
7	chr2:73821800-73830000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
9	chr2:73822600-73833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:73823000-73830000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
13	chr2:73825400-73833600	Weak transcription	Esophagus	oesophagus
14	chr2:73826000-73832200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:73826200-73833200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:73826800-73832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:73827000-73840600	Weak transcription	NHLF	lung
22	chr2:73827200-73831200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:73827200-73831600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:73827200-73837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:73827400-73830600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:73827400-73836400	Strong transcription	Primary T cells from cord blood	blood
27	chr2:73827600-73830600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:73827600-73830600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:73827600-73831800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:73827600-73832400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:73827600-73837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:73827600-73838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:73827800-73830000	Weak transcription	GM12878-XiMat	blood
35	chr2:73827800-73830400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:73827800-73830400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:73827800-73830600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr2:73827800-73830800	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:73827800-73831000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:73827800-73831000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:73827800-73831000	Strong transcription	Brain Cingulate Gyrus	brain
42	chr2:73827800-73831000	Strong transcription	Brain Hippocampus Middle	brain
43	chr2:73827800-73831000	Strong transcription	Fetal Stomach	stomach
44	chr2:73827800-73832200	Strong transcription	Fetal Intestine Large	intestine
45	chr2:73827800-73832200	Strong transcription	Left Ventricle	heart
46	chr2:73827800-73832200	Strong transcription	Dnd41	blood
47	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:73828000-73829600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:73828000-73829600	Strong transcription	Pancreas	Pancrea
50	chr2:73828000-73829800	Strong transcription	Gastric	stomach

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