Variant report

Variant	rs10189578
Chromosome Location	chr2:73728609-73728610
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs10190002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10207970	0.81[EUR][1000 genomes]
rs1052161	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1083919	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1083920	0.82[ASN][1000 genomes]
rs1083921	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1083922	0.81[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1083923	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1091568	0.85[ASN][1000 genomes]
rs11126399	1.00[CHB][hapmap]
rs11126402	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11685372	0.81[ASN][1000 genomes]
rs11688718	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1246094	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1246096	0.82[ASN][1000 genomes]
rs1246105	0.81[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs12618600	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap]
rs12620018	0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12620091	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs12991161	0.96[CEU][hapmap]
rs12995433	0.88[EUR][1000 genomes]
rs12996463	0.89[EUR][1000 genomes]
rs13009035	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13017182	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs13027816	0.96[CEU][hapmap]
rs1320374	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs13386124	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13399087	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1403412	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs1406105	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs1528169	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1881246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2037814	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs2091503	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091504	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2178154	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421489	0.92[CHB][hapmap]
rs2421545	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421546	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2421548	0.89[EUR][1000 genomes]
rs2421574	0.88[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2421581	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2421583	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2421586	0.96[CEU][hapmap];0.87[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs2421667	0.84[EUR][1000 genomes]
rs2421668	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs2421669	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2948441	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3820700	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs4346412	0.84[EUR][1000 genomes]
rs4511748	0.92[CHB][hapmap]
rs4852305	0.81[JPT][hapmap]
rs4852306	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4852308	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852927	0.87[EUR][1000 genomes]
rs4852951	0.95[CEU][hapmap]
rs4852954	0.88[CEU][hapmap];0.82[GIH][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap]
rs4852959	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap]
rs55677218	0.81[ASN][1000 genomes]
rs56770679	0.85[ASN][1000 genomes]
rs62153184	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546826	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs6546827	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6546829	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6546830	0.81[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6546842	0.85[ASN][1000 genomes]
rs6546846	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6546870	0.92[CHB][hapmap]
rs6706235	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs6710659	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6722867	0.89[EUR][1000 genomes]
rs6729468	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6730785	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6732440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs6742619	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs6743576	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6744697	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6745560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6746971	0.92[EUR][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs6749680	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6757996	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67898050	0.85[ASN][1000 genomes]
rs68154245	0.86[ASN][1000 genomes]
rs72811933	0.83[ASN][1000 genomes]
rs7562047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7566315	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570683	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs7574291	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs7576824	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs7585119	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7598660	0.92[CEU][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs7598901	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7606483	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7606947	0.88[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs7609249	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs780388	0.87[ASN][1000 genomes]
rs780389	0.87[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs780391	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs780393	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780394	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780395	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs802113	0.87[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10189578	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs10189578	ALMS1	cis	parietal	SCAN
rs10189578	DUSP11	cis	cerebellum	SCAN
rs10189578	ALMS1P	cis	cerebellum	SCAN
rs10189578	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs10189578	ALMS1P	cis	parietal	SCAN
rs10189578	LRRTM4	cis	cerebellum	SCAN
rs10189578	ALMS1	cis	cerebellum	SCAN
rs10189578	MXD1	cis	cerebellum	SCAN
rs10189578	DUSP11	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73707000-73733400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:73711800-73740400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:73715600-73740200	Weak transcription	Esophagus	oesophagus
5	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:73715800-73740200	Weak transcription	Gastric	stomach
7	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:73718000-73740800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:73718000-73746800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:73718200-73731800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:73718200-73740400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:73718400-73738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:73718400-73740200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:73718600-73732400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:73718600-73740200	Weak transcription	Fetal Kidney	kidney
16	chr2:73718600-73740400	Weak transcription	Thymus	Thymus
17	chr2:73718800-73730800	Weak transcription	Fetal Heart	heart
18	chr2:73718800-73731200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:73718800-73740200	Weak transcription	Aorta	Aorta
20	chr2:73718800-73740200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:73718800-73740400	Weak transcription	HSMMtube	muscle
22	chr2:73719000-73740200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:73719000-73740400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:73719200-73729400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:73719200-73730800	Weak transcription	Hela-S3	cervix
26	chr2:73719200-73731200	Weak transcription	Fetal Lung	lung
27	chr2:73719200-73731800	Weak transcription	Fetal Brain Female	brain
28	chr2:73719200-73739800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:73719200-73740200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:73719400-73731800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:73719400-73740400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:73719400-73747000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:73719600-73729400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:73719600-73738200	Weak transcription	Primary T cells from cord blood	blood
35	chr2:73719800-73731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:73719800-73731600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:73719800-73740200	Weak transcription	Primary B cells from cord blood	blood
38	chr2:73721800-73731400	Weak transcription	Dnd41	blood
39	chr2:73722000-73731200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:73725800-73731000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:73727600-73731200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:73727600-73731200	Weak transcription	HSMM	muscle
43	chr2:73728200-73747000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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