Variant report

Variant	rs13409668
Chromosome Location	chr2:73753187-73753188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10169213	0.88[EUR][1000 genomes]
rs10169714	0.88[EUR][1000 genomes]
rs10170786	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.86[EUR][1000 genomes]
rs10178678	0.93[EUR][1000 genomes]
rs10179134	0.86[EUR][1000 genomes]
rs10181563	0.84[EUR][1000 genomes]
rs10183818	0.93[EUR][1000 genomes]
rs10184268	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185080	0.89[EUR][1000 genomes]
rs10186501	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.93[EUR][1000 genomes]
rs10187416	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	0.90[EUR][1000 genomes]
rs10193972	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.89[EUR][1000 genomes]
rs10198549	0.88[EUR][1000 genomes]
rs10199224	0.94[EUR][1000 genomes]
rs10207220	0.88[EUR][1000 genomes]
rs10207264	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469966	0.84[EUR][1000 genomes]
rs10496191	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496193	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.88[EUR][1000 genomes]
rs11674602	0.92[EUR][1000 genomes]
rs11676385	0.93[EUR][1000 genomes]
rs11679809	0.84[EUR][1000 genomes]
rs11686019	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689588	0.91[EUR][1000 genomes]
rs11693586	0.92[EUR][1000 genomes]
rs11693588	0.92[EUR][1000 genomes]
rs11884776	0.95[EUR][1000 genomes]
rs11893881	0.84[EUR][1000 genomes]
rs11899740	0.86[EUR][1000 genomes]
rs11899902	0.85[EUR][1000 genomes]
rs11901272	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383871	0.86[EUR][1000 genomes]
rs13384952	0.93[EUR][1000 genomes]
rs13385564	0.90[EUR][1000 genomes]
rs13391258	1.00[ASN][1000 genomes]
rs13391552	0.87[EUR][1000 genomes]
rs13392691	0.96[EUR][1000 genomes]
rs13392872	0.91[EUR][1000 genomes]
rs13398956	0.93[EUR][1000 genomes]
rs13400985	0.93[EUR][1000 genomes]
rs13409366	0.82[EUR][1000 genomes]
rs13411311	0.92[EUR][1000 genomes]
rs13421462	0.93[EUR][1000 genomes]
rs13427832	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428235	0.85[EUR][1000 genomes]
rs13431267	0.86[EUR][1000 genomes]
rs13432605	0.86[EUR][1000 genomes]
rs1403284	0.93[EUR][1000 genomes]
rs1534471	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.88[EUR][1000 genomes]
rs17009159	0.88[EUR][1000 genomes]
rs1881245	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056486	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.94[EUR][1000 genomes]
rs2421555	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.86[EUR][1000 genomes]
rs2901438	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs56014217	0.86[EUR][1000 genomes]
rs56145559	0.81[EUR][1000 genomes]
rs56154726	0.93[EUR][1000 genomes]
rs56672945	0.86[EUR][1000 genomes]
rs58603761	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844734	0.86[EUR][1000 genomes]
rs62149781	0.83[EUR][1000 genomes]
rs62151646	0.92[EUR][1000 genomes]
rs62151652	0.92[EUR][1000 genomes]
rs6546835	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546854	0.83[EUR][1000 genomes]
rs6546856	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546858	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	1.00[ASN][1000 genomes]
rs6704782	0.90[EUR][1000 genomes]
rs6705489	0.91[EUR][1000 genomes]
rs6705977	1.00[ASN][1000 genomes]
rs6707722	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.92[EUR][1000 genomes]
rs6710438	0.86[EUR][1000 genomes]
rs6711001	1.00[ASN][1000 genomes]
rs6711033	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6718843	1.00[ASN][1000 genomes]
rs6719753	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.88[EUR][1000 genomes]
rs6736866	0.91[EUR][1000 genomes]
rs6740223	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.88[EUR][1000 genomes]
rs6741067	0.84[EUR][1000 genomes]
rs6745368	0.86[EUR][1000 genomes]
rs6745480	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753344	0.91[EUR][1000 genomes]
rs6755217	0.88[EUR][1000 genomes]
rs6755241	0.88[EUR][1000 genomes]
rs6756885	0.87[EUR][1000 genomes]
rs6756987	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73947808	0.93[EUR][1000 genomes]
rs7424690	0.87[EUR][1000 genomes]
rs7558944	0.86[EUR][1000 genomes]
rs7564890	0.89[EUR][1000 genomes]
rs7566364	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.93[EUR][1000 genomes]
rs7576245	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	0.86[EUR][1000 genomes]
rs7582606	0.86[EUR][1000 genomes]
rs7583255	0.88[EUR][1000 genomes]
rs7584575	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.88[EUR][1000 genomes]
rs7587577	0.83[EUR][1000 genomes]
rs7588169	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.91[EUR][1000 genomes]
rs7596773	0.82[EUR][1000 genomes]
rs7598396	0.91[EUR][1000 genomes]
rs7598419	0.88[EUR][1000 genomes]
rs7598946	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.93[EUR][1000 genomes]
rs7603647	0.87[EUR][1000 genomes]
rs7604682	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.87[EUR][1000 genomes]
rs9309473	0.95[EUR][1000 genomes]
rs9653557	0.88[EUR][1000 genomes]
rs9749859	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.86[EUR][1000 genomes]
rs9753079	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.83[AMR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13409668	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:73731600-73759000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
5	chr2:73736400-73761600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:73739400-73756400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:73740800-73753800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:73740800-73757600	Weak transcription	Ovary	ovary
9	chr2:73741000-73755000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:73741000-73755600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:73741000-73756200	Weak transcription	Fetal Intestine Small	intestine
12	chr2:73741000-73756400	Weak transcription	Thymus	Thymus
13	chr2:73741000-73757200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:73741000-73757400	Weak transcription	Aorta	Aorta
15	chr2:73741000-73757400	Weak transcription	Pancreas	Pancrea
16	chr2:73741000-73757600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:73741000-73757800	Weak transcription	Gastric	stomach
18	chr2:73741000-73758800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:73741000-73759400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:73741000-73767400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:73741200-73757400	Weak transcription	Fetal Stomach	stomach
22	chr2:73741200-73757600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:73744200-73759000	Weak transcription	HSMMtube	muscle
24	chr2:73744200-73799800	Weak transcription	NH-A	brain
25	chr2:73744600-73764400	Weak transcription	HSMM	muscle
26	chr2:73744800-73756600	Weak transcription	Fetal Brain Male	brain
27	chr2:73745400-73756200	Weak transcription	Fetal Thymus	thymus
28	chr2:73745600-73756400	Weak transcription	A549	lung
29	chr2:73745600-73757400	Weak transcription	Placenta	Placenta
30	chr2:73746000-73765200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:73746800-73757400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:73747800-73757600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:73747800-73786800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:73748000-73758800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:73748000-73762000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:73748200-73756200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:73748600-73753800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:73748800-73755600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:73749400-73756600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:73749400-73757800	Weak transcription	Left Ventricle	heart
41	chr2:73749600-73756400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:73750600-73753800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:73751600-73753200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr2:73751800-73753400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:73751800-73754200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr2:73751800-73759400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:73752000-73754200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:73752600-73753400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:73752600-73753800	Weak transcription	Dnd41	blood
50	chr2:73752600-73759800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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