Variant report

Variant	rs11126402
Chromosome Location	chr2:73776582-73776583
allele	C/G
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: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10189578	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10190002	1.00[CEU][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs1052161	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1083919	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1083921	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1083923	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10865398	0.96[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11688718	0.92[EUR][1000 genomes]
rs1246094	0.89[EUR][1000 genomes]
rs12618600	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs12620018	1.00[CEU][hapmap]
rs12620091	0.80[CEU][hapmap]
rs12991161	1.00[CEU][hapmap]
rs12995433	0.85[EUR][1000 genomes]
rs12996463	0.86[EUR][1000 genomes]
rs13008860	0.81[EUR][1000 genomes]
rs13009035	0.91[EUR][1000 genomes]
rs13017182	1.00[CEU][hapmap]
rs13027816	1.00[CEU][hapmap]
rs1320374	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13386124	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13399087	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1528169	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17349804	0.90[ASN][1000 genomes]
rs1881246	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs2037814	0.81[JPT][hapmap]
rs2091503	0.84[EUR][1000 genomes]
rs2091504	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2178154	0.88[EUR][1000 genomes]
rs2421545	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2421546	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs2421548	0.85[EUR][1000 genomes]
rs2421574	0.92[CEU][hapmap]
rs2421582	0.95[CEU][hapmap]
rs2421583	1.00[CEU][hapmap]
rs2421586	1.00[CEU][hapmap]
rs2421667	0.87[EUR][1000 genomes]
rs2421668	1.00[CEU][hapmap]
rs3820700	0.82[JPT][hapmap]
rs4346412	0.88[EUR][1000 genomes]
rs4852306	0.85[EUR][1000 genomes]
rs4852308	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4852927	0.84[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap]
rs4852954	0.92[CEU][hapmap]
rs4852959	1.00[CEU][hapmap]
rs62153184	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6546827	0.81[JPT][hapmap]
rs6546846	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6706409	0.81[JPT][hapmap]
rs6722867	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6729468	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6730785	0.88[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs6742619	0.92[CEU][hapmap]
rs6743576	0.93[EUR][1000 genomes]
rs6744697	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6745560	0.96[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6746971	0.88[EUR][1000 genomes]
rs6749680	0.84[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs6757996	0.95[EUR][1000 genomes]
rs7562047	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7566315	0.95[EUR][1000 genomes]
rs7570683	1.00[CEU][hapmap]
rs7585119	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606483	0.92[EUR][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs7609249	0.93[EUR][1000 genomes]
rs780390	0.82[JPT][hapmap]
rs780391	0.92[EUR][1000 genomes]
rs780393	0.91[EUR][1000 genomes]
rs780394	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs780395	0.83[AMR][1000 genomes];0.93[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11126402	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11126402	TPRKB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 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	chr2:73747800-73786800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:73758000-73799800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:73758200-73785800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:73758200-73800200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:73758400-73786800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
9	chr2:73760600-73828000	Weak transcription	Right Ventricle	heart
10	chr2:73760800-73787000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:73762000-73786600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:73763800-73785200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:73764200-73777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:73764200-73785000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:73764400-73785800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:73764600-73806800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:73764600-73807200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:73765200-73785000	Weak transcription	Fetal Kidney	kidney
19	chr2:73765200-73786600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:73765200-73807800	Weak transcription	Brain Anterior Caudate	brain
21	chr2:73765400-73786200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:73765400-73786200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:73765400-73786200	Weak transcription	HSMM	muscle
24	chr2:73765400-73792000	Weak transcription	HSMMtube	muscle
25	chr2:73765400-73808400	Weak transcription	HepG2	liver
26	chr2:73765600-73786200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:73765600-73786200	Weak transcription	Fetal Lung	lung
28	chr2:73765600-73787200	Weak transcription	A549	lung
29	chr2:73765600-73799600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:73765800-73777000	Weak transcription	Dnd41	blood
31	chr2:73765800-73777200	Weak transcription	Liver	Liver
32	chr2:73765800-73815400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
34	chr2:73766000-73777800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:73766000-73785000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:73766000-73786000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:73766000-73793400	Weak transcription	Aorta	Aorta
38	chr2:73766000-73807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:73766400-73778000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:73766400-73778200	Weak transcription	Fetal Intestine Small	intestine
41	chr2:73766400-73784200	Weak transcription	Left Ventricle	heart
42	chr2:73766400-73786000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:73766400-73786800	Weak transcription	Brain Germinal Matrix	brain
44	chr2:73766400-73799400	Weak transcription	Thymus	Thymus
45	chr2:73766400-73799600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:73766400-73799600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:73766400-73799600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:73766400-73799600	Weak transcription	Lung	lung
49	chr2:73766400-73803200	Weak transcription	Fetal Intestine Large	intestine
50	chr2:73767000-73784800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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