Variant report

Variant	rs1246096
Chromosome Location	chr2:73705088-73705089
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10165862	0.84[CHB][hapmap]
rs10189578	0.82[ASN][1000 genomes]
rs10190002	0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs10192125	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10197233	0.85[EUR][1000 genomes]
rs1052161	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1083919	0.84[ASN][1000 genomes]
rs1083920	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1083921	0.84[ASN][1000 genomes]
rs1083922	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1083923	0.89[ASN][1000 genomes]
rs10865398	0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1091568	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126399	0.84[CHB][hapmap]
rs11126407	0.86[EUR][1000 genomes]
rs11126408	0.85[EUR][1000 genomes]
rs11126409	0.84[EUR][1000 genomes]
rs11680056	0.85[EUR][1000 genomes]
rs11683970	0.86[EUR][1000 genomes]
rs11685372	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11689767	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12151671	0.86[EUR][1000 genomes]
rs1246094	0.90[ASN][1000 genomes]
rs1246105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12465867	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs12478871	0.85[CEU][hapmap]
rs12618600	0.97[CHD][hapmap];0.93[JPT][hapmap]
rs12620569	0.86[EUR][1000 genomes]
rs12713783	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13007306	0.85[EUR][1000 genomes]
rs13007623	0.86[EUR][1000 genomes]
rs13017182	0.91[CHD][hapmap]
rs1320374	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1403412	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs1406105	0.89[ASW][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17349804	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1852645	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1852646	0.85[EUR][1000 genomes]
rs1852647	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs1879662	0.85[EUR][1000 genomes]
rs1879666	0.86[EUR][1000 genomes]
rs1881246	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs1881247	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1881248	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2017116	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2037814	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091503	0.82[ASN][1000 genomes]
rs2091504	0.84[ASN][1000 genomes]
rs2178154	0.82[ASN][1000 genomes]
rs2280506	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2280507	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs2421545	0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2421546	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2421581	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2421582	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2421583	0.93[JPT][hapmap]
rs2421585	0.86[EUR][1000 genomes]
rs2421587	0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2421589	0.81[EUR][1000 genomes]
rs2421590	0.86[EUR][1000 genomes]
rs2421660	0.86[EUR][1000 genomes]
rs2421662	0.86[EUR][1000 genomes]
rs2421668	0.91[CHD][hapmap]
rs2421669	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2461691	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28708576	0.82[EUR][1000 genomes]
rs2948441	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2950770	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34719281	0.86[EUR][1000 genomes]
rs3820700	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3980696	0.83[EUR][1000 genomes]
rs4241256	0.86[EUR][1000 genomes]
rs4436991	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4443018	0.85[EUR][1000 genomes]
rs4511748	0.91[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs4852305	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4852306	0.80[ASN][1000 genomes]
rs4852309	0.84[EUR][1000 genomes]
rs4852310	0.86[EUR][1000 genomes]
rs4852311	0.90[CEU][hapmap]
rs4852936	0.92[EUR][1000 genomes]
rs4852937	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4852940	0.85[EUR][1000 genomes]
rs4852948	0.85[EUR][1000 genomes]
rs4852949	0.86[EUR][1000 genomes]
rs55677218	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56054150	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56068325	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56770679	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546826	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs6546829	0.84[CHB][hapmap]
rs6546830	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546831	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546832	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6546833	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546834	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546842	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6546863	0.86[EUR][1000 genomes]
rs6546865	0.86[EUR][1000 genomes]
rs6546870	0.91[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs66931335	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6706235	0.84[CHB][hapmap]
rs6706409	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs6710659	0.84[CHB][hapmap]
rs6712242	0.83[EUR][1000 genomes]
rs6725284	0.86[EUR][1000 genomes]
rs6729347	0.86[EUR][1000 genomes]
rs6732440	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs6734450	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6744273	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6745560	1.00[CHD][hapmap];0.87[JPT][hapmap]
rs6746458	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6746971	0.81[ASN][1000 genomes]
rs6747145	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs6748040	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs6749680	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6757996	0.82[ASN][1000 genomes]
rs6759464	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67877078	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67898050	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68154245	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72811933	0.86[ASN][1000 genomes]
rs72811939	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7562047	0.87[ASN][1000 genomes]
rs7570014	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7574291	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs7576824	0.84[CHB][hapmap];0.94[CHD][hapmap]
rs7579068	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7585119	0.87[ASN][1000 genomes]
rs7585668	0.85[EUR][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7607989	0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs7608308	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7609034	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs780388	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs780389	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs780390	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs780391	0.93[ASN][1000 genomes]
rs780393	0.92[ASN][1000 genomes]
rs780394	0.89[ASN][1000 genomes]
rs780395	0.89[ASN][1000 genomes]
rs780396	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs802113	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1246096	ALMS1P	cis	cerebellum	SCAN
rs1246096	ALMS1P	cis	parietal	SCAN
rs1246096	DUSP11	cis	cerebellum	SCAN
rs1246096	STAMBP	cis	multi-tissue	Pritchard
rs1246096	DUSP11	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73676200-73719400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:73676800-73706400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:73677000-73714200	Weak transcription	Pancreas	Pancrea
4	chr2:73678000-73706800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:73680200-73706400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:73680200-73714200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:73681600-73706800	Weak transcription	HSMM	muscle
8	chr2:73683000-73706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:73687000-73706200	Weak transcription	Primary T cells from cord blood	blood
10	chr2:73687000-73706400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:73688000-73714200	Weak transcription	Ovary	ovary
12	chr2:73688600-73706200	Weak transcription	Fetal Lung	lung
13	chr2:73695800-73706400	Weak transcription	Fetal Kidney	kidney
14	chr2:73697200-73706400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:73697600-73706200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:73697600-73717800	Weak transcription	Fetal Heart	heart
17	chr2:73700000-73713800	Weak transcription	Thymus	Thymus
18	chr2:73700200-73706200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:73700200-73706400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:73700800-73706400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:73701200-73706400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:73701600-73706000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:73701800-73716800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:73702400-73706000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:73702400-73706200	Weak transcription	Dnd41	blood
26	chr2:73702400-73716600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:73703000-73706400	Weak transcription	Primary B cells from cord blood	blood
28	chr2:73703600-73706200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:73703800-73706000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:73704400-73714000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:73704600-73716800	Weak transcription	HSMMtube	muscle
32	chr2:73704600-73721000	Weak transcription	HMEC	breast
33	chr2:73704800-73716800	Weak transcription	Brain Angular Gyrus	brain
34	chr2:73704800-73718600	Weak transcription	Placenta Amnion	Placenta Amnion

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