Variant report

Variant	rs2421667
Chromosome Location	chr2:73832459-73832460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10189578	0.84[EUR][1000 genomes]
rs10190002	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052161	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1083919	0.83[EUR][1000 genomes]
rs1083921	0.83[EUR][1000 genomes]
rs1083922	0.84[EUR][1000 genomes]
rs1083923	0.83[EUR][1000 genomes]
rs10865398	0.84[EUR][1000 genomes]
rs11126402	0.87[EUR][1000 genomes]
rs11688718	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1246094	0.85[EUR][1000 genomes]
rs12620018	0.81[EUR][1000 genomes]
rs12991161	0.81[EUR][1000 genomes]
rs12996463	0.83[EUR][1000 genomes]
rs13009035	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13027816	0.82[EUR][1000 genomes]
rs1320374	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13386124	0.86[EUR][1000 genomes]
rs13399087	0.85[EUR][1000 genomes]
rs1528169	0.83[EUR][1000 genomes]
rs1881246	0.83[EUR][1000 genomes]
rs2091504	0.83[EUR][1000 genomes]
rs2178154	0.86[EUR][1000 genomes]
rs2421545	0.80[EUR][1000 genomes]
rs2421548	0.80[EUR][1000 genomes]
rs2421582	0.82[EUR][1000 genomes]
rs2421583	0.82[EUR][1000 genomes]
rs2421584	0.82[EUR][1000 genomes]
rs2421586	0.82[EUR][1000 genomes]
rs2948441	0.92[ASN][1000 genomes]
rs34874205	0.82[AMR][1000 genomes]
rs4346412	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4436991	0.92[ASN][1000 genomes]
rs4852308	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4852939	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4852951	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4852954	0.81[AMR][1000 genomes]
rs56054150	0.86[ASN][1000 genomes]
rs62153184	0.86[EUR][1000 genomes]
rs6546846	0.84[EUR][1000 genomes]
rs6546862	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6722867	0.94[EUR][1000 genomes]
rs6729468	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6732440	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743576	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6744697	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6745560	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6746971	0.86[EUR][1000 genomes]
rs6755948	0.84[AMR][1000 genomes]
rs6757996	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72811939	0.80[ASN][1000 genomes]
rs7562047	0.84[EUR][1000 genomes]
rs7566315	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570014	0.94[ASN][1000 genomes]
rs7570683	0.82[EUR][1000 genomes]
rs7574240	0.81[EUR][1000 genomes]
rs7574268	0.81[EUR][1000 genomes]
rs7585119	0.84[EUR][1000 genomes]
rs7598901	0.83[EUR][1000 genomes]
rs7606483	0.81[EUR][1000 genomes]
rs7609034	0.95[ASN][1000 genomes]
rs7609249	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs780391	0.87[EUR][1000 genomes]
rs780393	0.86[EUR][1000 genomes]
rs780394	0.83[EUR][1000 genomes]
rs780395	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv961795	chr2:73830604-73834098	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2421667	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2421667	ALMS1P	cis	Nerve Tibial	GTEx
rs2421667	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2421667	ALMS1P	cis	Whole Blood	GTEx

Chromatin state (count:104 , 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	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
6	chr2:73822600-73833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:73825400-73833600	Weak transcription	Esophagus	oesophagus
10	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:73826200-73833200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:73826800-73832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:73827000-73840600	Weak transcription	NHLF	lung
17	chr2:73827200-73837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:73827400-73836400	Strong transcription	Primary T cells from cord blood	blood
19	chr2:73827600-73837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:73827600-73838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:73828800-73837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:73829000-73837600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:73829000-73839000	Weak transcription	NHDF-Ad	bronchial
26	chr2:73829000-73839400	Weak transcription	Placenta	Placenta
27	chr2:73829200-73838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:73829200-73840000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:73829600-73833600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:73829600-73835600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:73829600-73837200	Weak transcription	Lung	lung
33	chr2:73829600-73837600	Weak transcription	Pancreas	Pancrea
34	chr2:73829600-73840200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:73829800-73835400	Weak transcription	Right Ventricle	heart
36	chr2:73829800-73838000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:73829800-73839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:73829800-73840000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:73829800-73840000	Weak transcription	Gastric	stomach
40	chr2:73829800-73840400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:73830000-73840800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:73830200-73838000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:73830400-73835400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:73830400-73835600	Weak transcription	Brain Anterior Caudate	brain
45	chr2:73830400-73835800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:73830400-73839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:73830400-73843600	Weak transcription	Aorta	Aorta
48	chr2:73830600-73833800	Weak transcription	Fetal Brain Female	brain
49	chr2:73830600-73834000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:73830600-73835400	Weak transcription	Fetal Thymus	thymus

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