Variant report

Variant	rs780390
Chromosome Location	chr2:73714933-73714934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73612210..73615081-chr2:73714696..73716979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 152 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap]
rs10189578	0.85[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10192125	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10197233	0.83[EUR][1000 genomes]
rs1052161	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1083919	0.86[ASN][1000 genomes]
rs1083920	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1083921	0.84[ASN][1000 genomes]
rs1083922	0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1083923	0.85[ASN][1000 genomes]
rs10865398	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1091568	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11126399	1.00[CHB][hapmap]
rs11126407	0.84[EUR][1000 genomes]
rs11126408	0.83[EUR][1000 genomes]
rs11126409	0.84[EUR][1000 genomes]
rs11680056	0.83[EUR][1000 genomes]
rs11683970	0.84[EUR][1000 genomes]
rs11685372	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688718	0.81[ASN][1000 genomes]
rs11689767	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12151671	0.84[EUR][1000 genomes]
rs1246094	0.88[ASN][1000 genomes]
rs1246096	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246105	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs12478871	0.85[CEU][hapmap]
rs12618600	0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs12620018	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12620091	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12620569	0.84[EUR][1000 genomes]
rs12713783	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13007306	0.83[EUR][1000 genomes]
rs13007623	0.84[EUR][1000 genomes]
rs13017182	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs1320374	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1403412	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs1406105	0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17349804	0.92[EUR][1000 genomes]
rs1852645	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1852646	0.85[EUR][1000 genomes]
rs1852647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs1879662	0.83[EUR][1000 genomes]
rs1879666	0.84[EUR][1000 genomes]
rs1881246	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1881247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1881248	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2017116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2091504	0.80[ASN][1000 genomes]
rs2178154	0.81[ASN][1000 genomes]
rs2280506	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2280507	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2421489	0.92[CHB][hapmap]
rs2421545	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2421546	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2421581	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2421582	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2421583	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2421585	0.84[EUR][1000 genomes]
rs2421587	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2421590	0.84[EUR][1000 genomes]
rs2421660	0.84[EUR][1000 genomes]
rs2421662	0.84[EUR][1000 genomes]
rs2421668	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs2421669	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2461691	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28708576	0.81[EUR][1000 genomes]
rs2948441	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2950770	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34719281	0.84[EUR][1000 genomes]
rs3820700	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3980696	0.81[EUR][1000 genomes]
rs4241256	0.84[EUR][1000 genomes]
rs4436991	0.89[EUR][1000 genomes]
rs4443018	0.83[EUR][1000 genomes]
rs4511748	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4852305	1.00[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4852309	0.82[EUR][1000 genomes]
rs4852310	0.84[EUR][1000 genomes]
rs4852311	0.90[CEU][hapmap]
rs4852936	0.90[EUR][1000 genomes]
rs4852937	0.91[EUR][1000 genomes]
rs4852940	0.83[EUR][1000 genomes]
rs4852948	0.83[EUR][1000 genomes]
rs4852949	0.84[EUR][1000 genomes]
rs4852959	0.92[CHB][hapmap]
rs55677218	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56054150	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56068325	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56770679	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546826	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs6546827	0.92[CHB][hapmap]
rs6546829	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6546830	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546831	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6546833	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6546834	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546842	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546863	0.84[EUR][1000 genomes]
rs6546865	0.84[EUR][1000 genomes]
rs6546870	0.91[CEU][hapmap];0.92[CHB][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs66931335	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6706235	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs6710659	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6712242	0.81[EUR][1000 genomes]
rs6725284	0.84[EUR][1000 genomes]
rs6729347	0.84[EUR][1000 genomes]
rs6732440	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6734450	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742619	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6743576	0.81[ASN][1000 genomes]
rs6744273	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6745560	0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs6746458	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs6749680	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs6757996	0.81[ASN][1000 genomes]
rs6759464	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67877078	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67898050	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68154245	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72811933	0.89[ASN][1000 genomes]
rs72811939	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7562047	0.91[ASN][1000 genomes]
rs7566315	0.83[ASN][1000 genomes]
rs7570014	0.89[EUR][1000 genomes]
rs7574291	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs7576824	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs7579068	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7585119	0.91[ASN][1000 genomes]
rs7585668	0.83[EUR][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs7599323	0.80[CHD][hapmap]
rs7606483	0.81[ASN][1000 genomes]
rs7607989	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs7608308	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7609034	0.90[EUR][1000 genomes]
rs7609249	0.81[ASN][1000 genomes]
rs780388	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs780389	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs780391	0.88[ASN][1000 genomes]
rs780392	0.82[YRI][hapmap]
rs780393	0.89[ASN][1000 genomes]
rs780394	0.85[ASN][1000 genomes]
rs780395	0.85[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs802113	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs780390	DUSP11	cis	cerebellum	SCAN
rs780390	STAMBP	cis	multi-tissue	Pritchard
rs780390	DUSP11	cis	parietal	SCAN
rs780390	ALMS1P	cis	parietal	SCAN
rs780390	ALMS1P	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73676200-73719400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:73697600-73717800	Weak transcription	Fetal Heart	heart
3	chr2:73701800-73716800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:73702400-73716600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:73704600-73716800	Weak transcription	HSMMtube	muscle
6	chr2:73704600-73721000	Weak transcription	HMEC	breast
7	chr2:73704800-73716800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:73704800-73718600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:73705800-73722600	Weak transcription	Brain Substantia Nigra	brain
10	chr2:73706600-73715000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:73706600-73721000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:73706800-73716800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:73706800-73717000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:73707000-73715400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:73707000-73716400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:73707000-73716800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:73707000-73716800	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:73707000-73716800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:73707000-73717000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:73707000-73718000	Weak transcription	Fetal Kidney	kidney
21	chr2:73707000-73718000	Weak transcription	A549	lung
22	chr2:73707000-73733400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:73709200-73725400	Weak transcription	Fetal Brain Male	brain
24	chr2:73711800-73740400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:73712200-73716600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:73712600-73715200	Weak transcription	Colonic Mucosa	Colon
27	chr2:73712600-73716800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:73712600-73716800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:73712800-73716200	Weak transcription	HepG2	liver
30	chr2:73712800-73716600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:73712800-73716800	Weak transcription	Left Ventricle	heart
32	chr2:73712800-73717000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:73713000-73721000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:73713000-73721000	Weak transcription	Small Intestine	intestine
35	chr2:73713200-73715400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:73713200-73716800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:73713400-73715000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:73713400-73715000	Strong transcription	Fetal Lung	lung
40	chr2:73713400-73715200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:73713400-73715200	Strong transcription	Fetal Muscle Leg	muscle
42	chr2:73713400-73715200	ZNF genes & repeats	Dnd41	blood
43	chr2:73713400-73715400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr2:73713400-73715400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:73713400-73721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:73713600-73715200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:73713600-73715400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:73713600-73715400	ZNF genes & repeats	Brain Germinal Matrix	brain
49	chr2:73713600-73715400	ZNF genes & repeats	Fetal Brain Female	brain
50	chr2:73713600-73716800	Weak transcription	H9 Cell Line	embryonic stem cell

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