Variant report

Variant	rs11126404
Chromosome Location	chr2:73796924-73796925
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10169213	0.89[EUR][1000 genomes]
rs10169714	0.88[EUR][1000 genomes]
rs10170786	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.87[EUR][1000 genomes]
rs10178678	0.82[EUR][1000 genomes]
rs10181563	0.93[EUR][1000 genomes]
rs10183818	0.81[EUR][1000 genomes]
rs10184268	1.00[ASN][1000 genomes]
rs10185080	0.88[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];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.88[EUR][1000 genomes]
rs10198549	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs10199224	0.81[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	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496191	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.89[EUR][1000 genomes]
rs11676385	0.81[EUR][1000 genomes]
rs11686019	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	1.00[ASN][1000 genomes]
rs11689588	0.87[EUR][1000 genomes]
rs11884776	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs11893881	0.83[EUR][1000 genomes]
rs11901272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.81[EUR][1000 genomes]
rs13391258	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391552	0.86[EUR][1000 genomes]
rs13392691	0.82[EUR][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13400985	0.81[EUR][1000 genomes]
rs13409366	0.83[EUR][1000 genomes]
rs13409668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	0.94[CEU][hapmap]
rs13421462	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13427832	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431267	0.86[EUR][1000 genomes]
rs13432605	0.87[EUR][1000 genomes]
rs13538	0.94[CEU][hapmap]
rs1403284	0.81[EUR][1000 genomes]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[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];1.00[JPT][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];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[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	0.81[EUR][1000 genomes]
rs2421555	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.86[EUR][1000 genomes]
rs2901438	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56154726	0.81[EUR][1000 genomes]
rs58603761	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149781	0.83[EUR][1000 genomes]
rs6546827	0.88[CEU][hapmap]
rs6546835	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546854	0.83[EUR][1000 genomes]
rs6546856	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6546858	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	1.00[CEU][hapmap]
rs6705977	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707722	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710438	0.85[EUR][1000 genomes]
rs6711001	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711033	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6718843	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719753	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.89[EUR][1000 genomes]
rs6740223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.89[EUR][1000 genomes]
rs6745368	0.87[EUR][1000 genomes]
rs6745480	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	0.94[CEU][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	0.81[EUR][1000 genomes]
rs7424690	0.86[EUR][1000 genomes]
rs7558944	0.87[EUR][1000 genomes]
rs7566364	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.81[EUR][1000 genomes]
rs7576245	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][hapmap]
rs7582606	0.87[EUR][1000 genomes]
rs7583255	0.89[EUR][1000 genomes]
rs7584575	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.89[EUR][1000 genomes]
rs7587577	0.83[EUR][1000 genomes]
rs7588169	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	1.00[CEU][hapmap]
rs7596773	0.83[EUR][1000 genomes]
rs7598419	0.89[EUR][1000 genomes]
rs7598946	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.81[EUR][1000 genomes]
rs7603647	0.86[EUR][1000 genomes]
rs7604682	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.86[EUR][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs9653557	0.89[EUR][1000 genomes]
rs9749859	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.87[EUR][1000 genomes]
rs9753079	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11126404	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs11126404	ALMS1	cis	normal skin	skin_eQTL
rs11126404	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11126404	ALMS1P	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
2	chr2:73744200-73799800	Weak transcription	NH-A	brain
3	chr2:73758000-73799800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:73758200-73800200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
6	chr2:73760600-73828000	Weak transcription	Right Ventricle	heart
7	chr2:73764600-73806800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:73764600-73807200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:73765200-73807800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:73765400-73808400	Weak transcription	HepG2	liver
11	chr2:73765600-73799600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:73765800-73815400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
14	chr2:73766000-73807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:73766400-73799400	Weak transcription	Thymus	Thymus
16	chr2:73766400-73799600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:73766400-73799600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:73766400-73799600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:73766400-73799600	Weak transcription	Lung	lung
20	chr2:73766400-73803200	Weak transcription	Fetal Intestine Large	intestine
21	chr2:73769200-73802800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:73772000-73799600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:73772200-73799400	Weak transcription	Fetal Brain Female	brain
24	chr2:73775600-73811400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:73776000-73799600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:73776000-73801200	Weak transcription	GM12878-XiMat	blood
27	chr2:73776000-73821600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:73776400-73807800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:73778600-73799800	Weak transcription	Fetal Stomach	stomach
30	chr2:73778600-73811400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:73778800-73806200	Weak transcription	Fetal Intestine Small	intestine
32	chr2:73779800-73799400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:73779800-73799800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:73782200-73811400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:73782600-73808000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:73783600-73799800	Weak transcription	Primary B cells from cord blood	blood
37	chr2:73784200-73808200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr2:73784400-73799600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:73784400-73799800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:73785200-73815400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
42	chr2:73785600-73799800	Weak transcription	Left Ventricle	heart
43	chr2:73786000-73800200	Weak transcription	HMEC	breast
44	chr2:73786200-73799400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:73786200-73815400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:73786400-73799400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:73786400-73799600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:73786400-73800400	Weak transcription	Brain Substantia Nigra	brain
49	chr2:73786600-73800200	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:73787200-73799000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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