Variant report

Variant	rs11688718
Chromosome Location	chr2:73760939-73760940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73759257..73763158-chr2:73774216..73777787,3	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10165862	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10189578	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10190002	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1052161	0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1083919	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1083921	0.91[EUR][1000 genomes]
rs1083922	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs1083923	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865398	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1091568	0.81[ASN][1000 genomes]
rs11126399	0.92[CHB][hapmap]
rs11126402	0.92[EUR][1000 genomes]
rs11685372	0.93[ASN][1000 genomes]
rs11689767	0.91[ASN][1000 genomes]
rs1246094	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12465867	0.92[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs12618600	0.91[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs12620018	0.95[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs12620091	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs12991161	0.95[CEU][hapmap];0.81[YRI][hapmap]
rs12995433	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12996463	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13009035	0.84[EUR][1000 genomes]
rs13017182	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs13027816	0.95[CEU][hapmap]
rs1320374	0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs13386124	0.93[EUR][1000 genomes]
rs13399087	0.92[EUR][1000 genomes]
rs1403412	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs1406105	0.83[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs1528169	0.90[EUR][1000 genomes]
rs1852647	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs1881246	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2017116	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2037814	0.92[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2091503	0.82[EUR][1000 genomes]
rs2091504	0.91[EUR][1000 genomes]
rs2178154	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2421489	0.83[CHB][hapmap]
rs2421545	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421546	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs2421548	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2421574	0.87[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs2421581	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2421583	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2421586	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs2421667	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421668	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs2421669	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs2948441	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs3820700	0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs4346412	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4511748	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4852305	0.87[JPT][hapmap]
rs4852306	0.83[EUR][1000 genomes]
rs4852308	0.84[EUR][1000 genomes]
rs4852927	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4852951	0.95[CEU][hapmap];0.81[YRI][hapmap]
rs4852954	0.86[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4852959	0.95[CEU][hapmap];0.83[CHB][hapmap]
rs4852976	0.81[TSI][hapmap]
rs55677218	0.93[ASN][1000 genomes]
rs56054150	0.88[ASN][1000 genomes]
rs56068325	0.89[ASN][1000 genomes]
rs56770679	0.83[ASN][1000 genomes]
rs62153184	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546826	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs6546827	0.83[CHB][hapmap]
rs6546829	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6546832	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6546842	0.87[ASN][1000 genomes]
rs6546846	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546870	0.83[CHB][hapmap]
rs66931335	0.92[ASN][1000 genomes]
rs6706235	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6706409	0.92[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap]
rs6710659	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6722867	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6729468	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6730785	0.88[EUR][1000 genomes]
rs6732440	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742619	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6743576	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6744697	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745560	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746971	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6747145	0.92[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs6748040	0.92[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs6749680	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs6757996	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67877078	0.90[ASN][1000 genomes]
rs67898050	0.87[ASN][1000 genomes]
rs68154245	0.88[ASN][1000 genomes]
rs72811939	0.95[ASN][1000 genomes]
rs7562047	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7566315	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570683	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7574291	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs7576824	0.92[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs7585119	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7598660	0.91[CEU][hapmap]
rs7598901	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7606483	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7606947	0.87[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs7608308	0.90[ASN][1000 genomes]
rs7609249	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs780388	0.83[ASN][1000 genomes]
rs780389	0.83[ASN][1000 genomes]
rs780390	0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs780391	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs780393	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs780394	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs780395	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs780396	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs802113	0.83[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11688718	LRRTM4	cis	cerebellum	SCAN
rs11688718	DUSP11	cis	parietal	SCAN
rs11688718	ALMS1	cis	cerebellum	SCAN
rs11688718	ALMS1	cis	multi-tissue	Pritchard
rs11688718	ALMS1P	cis	parietal	SCAN
rs11688718	ALMS1P	cis	Nerve Tibial	GTEx
rs11688718	DUSP11	cis	cerebellum	SCAN
rs11688718	MXD1	cis	cerebellum	SCAN
rs11688718	RAB11FIP5	cis	brain	seeQTL
rs11688718	ALMS1	cis	brain	seeQTL
rs11688718	ALMS1	cis	parietal	SCAN
rs11688718	DCTN1	cis	brain	seeQTL
rs11688718	ALMS1P	cis	cerebellum	SCAN
rs11688718	CGI-121	cis	multi-tissue	Pritchard
rs11688718	HIST1H2BE	trans	brain	seeQTL
rs11688718	ALMS1	trans	brain	seeQTL
rs11688718	SEMA4F	trans	brain	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
2	chr2:73736400-73761600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:73741000-73767400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:73744200-73799800	Weak transcription	NH-A	brain
5	chr2:73744600-73764400	Weak transcription	HSMM	muscle
6	chr2:73746000-73765200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:73747800-73786800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:73748000-73762000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:73752600-73762600	Weak transcription	Fetal Kidney	kidney
10	chr2:73754600-73762000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:73756000-73766800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:73756400-73765000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:73756800-73764000	Weak transcription	Fetal Brain Male	brain
14	chr2:73757000-73764200	Weak transcription	K562	blood
15	chr2:73757000-73764600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:73757800-73764400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:73757800-73764600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:73758000-73765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:73758000-73799800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:73758200-73762000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:73758200-73764200	Strong transcription	Dnd41	blood
22	chr2:73758200-73764400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:73758200-73764400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:73758200-73764400	Weak transcription	HepG2	liver
25	chr2:73758200-73765000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:73758200-73766000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:73758200-73785800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:73758200-73800200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:73758400-73761000	Weak transcription	Spleen	Spleen
30	chr2:73758400-73764800	Weak transcription	Small Intestine	intestine
31	chr2:73758400-73765000	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:73758400-73786800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:73758600-73761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:73758600-73763800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:73758800-73761800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:73758800-73764000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:73759000-73761000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:73759000-73761000	Weak transcription	Esophagus	oesophagus
39	chr2:73759000-73761200	Weak transcription	Osteobl	bone
40	chr2:73759400-73762000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:73759400-73762600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:73759400-73765200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:73759400-73774200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:73759600-73761800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:73759600-73762000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:73759600-73763200	Weak transcription	GM12878-XiMat	blood
47	chr2:73759600-73764400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
49	chr2:73759800-73762600	Weak transcription	Fetal Lung	lung
50	chr2:73759800-73762600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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