Variant report

Variant	rs1320374
Chromosome Location	chr2:73828310-73828311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10189578	0.85[EUR][1000 genomes]
rs10190002	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1052161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1083919	0.85[EUR][1000 genomes]
rs1083921	0.83[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1083923	0.84[EUR][1000 genomes]
rs10865398	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11126402	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11126413	0.80[EUR][1000 genomes]
rs11126414	0.81[TSI][hapmap]
rs11126417	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11688718	0.88[EUR][1000 genomes]
rs11894953	0.81[TSI][hapmap]
rs1246094	0.86[EUR][1000 genomes]
rs12466032	0.88[YRI][hapmap]
rs12618600	0.96[CEU][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap]
rs12620018	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs12620091	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs12713793	0.81[TSI][hapmap]
rs12713798	0.81[TSI][hapmap]
rs12991161	1.00[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs12995433	0.81[EUR][1000 genomes]
rs12996463	0.82[EUR][1000 genomes]
rs13009035	0.95[EUR][1000 genomes]
rs13017182	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs13027816	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13386124	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13399087	0.87[EUR][1000 genomes]
rs1528169	0.82[EUR][1000 genomes]
rs17349804	0.80[ASN][1000 genomes]
rs17350188	0.81[TSI][hapmap]
rs1881246	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs1881247	0.85[JPT][hapmap]
rs2017116	0.87[JPT][hapmap]
rs2037814	0.87[JPT][hapmap]
rs2091504	0.83[EUR][1000 genomes]
rs2178154	0.85[EUR][1000 genomes]
rs2421545	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2421546	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2421548	0.82[EUR][1000 genomes]
rs2421574	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2421581	0.87[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs2421583	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs2421584	0.82[EUR][1000 genomes]
rs2421586	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2421667	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421668	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs2421669	0.87[JPT][hapmap]
rs2421674	0.81[TSI][hapmap]
rs2421676	0.81[TSI][hapmap]
rs2948441	0.87[JPT][hapmap]
rs34874205	0.83[AMR][1000 genomes]
rs3820700	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs4346412	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4852305	0.81[JPT][hapmap]
rs4852308	0.95[EUR][1000 genomes]
rs4852927	0.80[EUR][1000 genomes]
rs4852936	0.95[ASN][1000 genomes]
rs4852939	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4852954	0.92[CEU][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs4852959	1.00[CEU][hapmap]
rs4852975	0.81[TSI][hapmap]
rs4852976	0.86[TSI][hapmap]
rs62153184	0.88[EUR][1000 genomes]
rs6546832	0.87[JPT][hapmap]
rs6546846	0.86[EUR][1000 genomes]
rs6546862	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6722867	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6729468	0.86[EUR][1000 genomes]
rs6730785	0.80[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6742619	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs6743576	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6744697	0.87[EUR][1000 genomes]
rs6745560	0.83[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6746971	0.85[EUR][1000 genomes]
rs6749680	0.83[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap]
rs6755948	0.85[AMR][1000 genomes]
rs6757996	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7562047	0.86[EUR][1000 genomes]
rs7566315	0.94[EUR][1000 genomes]
rs7570683	1.00[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs7574240	0.81[EUR][1000 genomes]
rs7574268	0.81[EUR][1000 genomes]
rs7585119	0.86[EUR][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7598901	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7606483	0.83[EUR][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs7609249	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs780390	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs780391	0.88[EUR][1000 genomes]
rs780393	0.87[EUR][1000 genomes]
rs780394	0.84[EUR][1000 genomes]
rs780395	0.84[EUR][1000 genomes]
rs780396	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1320374	ALMS1P	cis	cerebellum	SCAN
rs1320374	DUSP11	cis	parietal	SCAN
rs1320374	LRRTM4	cis	cerebellum	SCAN
rs1320374	DUSP11	cis	cerebellum	SCAN
rs1320374	ALMS1	cis	cerebellum	SCAN
rs1320374	MPHOSPH10	cis	cerebellum	SCAN
rs1320374	MXD1	cis	cerebellum	SCAN
rs1320374	ALMS1	cis	parietal	SCAN
rs1320374	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs1320374	ALMS1P	cis	Nerve Tibial	GTEx
rs1320374	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1320374	ALMS1P	cis	Whole Blood	GTEx
rs1320374	ALMS1P	cis	parietal	SCAN

Chromatin state (count:108 , 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	chr2:73792200-73828600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:73797400-73828400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:73800600-73828400	Weak transcription	Aorta	Aorta
6	chr2:73800600-73828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:73800800-73828800	Weak transcription	HSMM	muscle
8	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
9	chr2:73807600-73829200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:73812800-73828600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:73815600-73828400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:73815600-73828400	Weak transcription	Brain Anterior Caudate	brain
13	chr2:73815600-73836000	Weak transcription	A549	lung
14	chr2:73816000-73829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:73819600-73829400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:73820600-73828400	Weak transcription	Spleen	Spleen
17	chr2:73821000-73828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:73821600-73830000	Weak transcription	Osteobl	bone
19	chr2:73821800-73828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:73821800-73830000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:73822000-73828600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
23	chr2:73822600-73833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:73822800-73828400	Weak transcription	HSMMtube	muscle
26	chr2:73823000-73828400	Weak transcription	Brain Germinal Matrix	brain
27	chr2:73823000-73828400	Weak transcription	Fetal Lung	lung
28	chr2:73823000-73830000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
30	chr2:73825000-73828400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:73825400-73833600	Weak transcription	Esophagus	oesophagus
32	chr2:73826000-73832200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:73826200-73828400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:73826200-73828400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:73826200-73829200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:73826200-73833200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:73826600-73828400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:73826600-73828600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:73826800-73828400	Weak transcription	Colonic Mucosa	Colon
43	chr2:73826800-73828600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:73826800-73828800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:73826800-73829200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:73826800-73832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:73827000-73840600	Weak transcription	NHLF	lung
49	chr2:73827200-73831200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:73827200-73831600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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