Variant report

Variant	rs3820700
Chromosome Location	chr2:73716810-73716811
allele	C/T
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: 157 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap]
rs10189578	0.87[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10192125	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197233	0.85[EUR][1000 genomes]
rs10519309	0.81[ASN][1000 genomes]
rs1052161	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1083919	0.88[ASN][1000 genomes]
rs1083920	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1083921	0.85[ASN][1000 genomes]
rs1083922	0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1083923	0.87[ASN][1000 genomes]
rs10865398	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1091568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11126399	1.00[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11688718	0.83[ASN][1000 genomes]
rs11689767	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12151671	0.86[EUR][1000 genomes]
rs1246094	0.90[ASN][1000 genomes]
rs1246096	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1246105	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	0.86[EUR][1000 genomes]
rs12713783	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13007306	0.85[EUR][1000 genomes]
rs13007623	0.86[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];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17349804	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1852645	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1852646	0.85[EUR][1000 genomes]
rs1852647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879662	0.85[EUR][1000 genomes]
rs1879666	0.86[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1881248	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2017116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091503	0.80[ASN][1000 genomes]
rs2091504	0.82[ASN][1000 genomes]
rs2178154	0.83[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]
rs2421489	0.92[CHB][hapmap]
rs2421545	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[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	0.86[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	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs2421669	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2461691	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28708576	0.82[EUR][1000 genomes]
rs2948441	0.91[CEU][hapmap];1.00[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]
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];0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs4852305	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][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]
rs4852959	0.92[CHB][hapmap]
rs55677218	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56054150	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56068325	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56770679	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6546831	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6546832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546833	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6546834	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546842	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546863	0.86[EUR][1000 genomes]
rs6546865	0.86[EUR][1000 genomes]
rs6546870	0.91[CEU][hapmap];0.92[CHB][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs66931335	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	0.83[EUR][1000 genomes]
rs6725284	0.86[EUR][1000 genomes]
rs6729347	0.86[EUR][1000 genomes]
rs6729468	0.81[ASN][1000 genomes]
rs6732440	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6734450	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6742619	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6743576	0.82[ASN][1000 genomes]
rs6744273	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6745560	0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs6746458	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6746971	0.81[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	0.83[ASN][1000 genomes]
rs6759464	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67877078	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67898050	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68154245	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72811933	0.91[ASN][1000 genomes]
rs72811939	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562047	0.93[ASN][1000 genomes]
rs7566315	0.85[ASN][1000 genomes]
rs7570014	0.82[AMR][1000 genomes];0.91[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];0.83[EUR][1000 genomes]
rs7585119	0.93[ASN][1000 genomes]
rs7585668	0.85[EUR][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7599323	0.80[CHD][hapmap]
rs7606483	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];0.88[ASN][1000 genomes]
rs7609034	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7609249	0.82[ASN][1000 genomes]
rs780388	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs780389	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs780390	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]
rs780391	0.90[ASN][1000 genomes]
rs780392	0.82[YRI][hapmap]
rs780393	0.91[ASN][1000 genomes]
rs780394	0.87[ASN][1000 genomes]
rs780395	0.87[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs802113	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3820700	STAMBP	cis	multi-tissue	Pritchard
rs3820700	DUSP11	cis	parietal	SCAN
rs3820700	DUSP11	cis	cerebellum	SCAN
rs3820700	ALMS1P	cis	parietal	SCAN
rs3820700	ALMS1P	cis	cerebellum	SCAN

Chromatin state (count:113 , 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	chr2:73704600-73721000	Weak transcription	HMEC	breast
4	chr2:73704800-73718600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:73705800-73722600	Weak transcription	Brain Substantia Nigra	brain
6	chr2:73706600-73721000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:73706800-73717000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:73707000-73717000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:73707000-73718000	Weak transcription	Fetal Kidney	kidney
10	chr2:73707000-73718000	Weak transcription	A549	lung
11	chr2:73707000-73733400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:73709200-73725400	Weak transcription	Fetal Brain Male	brain
13	chr2:73711800-73740400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:73712800-73717000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:73713000-73721000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:73713000-73721000	Weak transcription	Small Intestine	intestine
17	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:73713400-73721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:73713800-73719600	Strong transcription	Primary T cells from cord blood	blood
20	chr2:73714000-73719200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:73714400-73717000	Weak transcription	NH-A	brain
22	chr2:73714600-73717000	Weak transcription	Placenta	Placenta
23	chr2:73714600-73718600	Strong transcription	Right Ventricle	heart
24	chr2:73714600-73719200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:73714600-73721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:73714600-73725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:73714800-73718800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr2:73714800-73721200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:73714800-73722200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:73715000-73717000	Weak transcription	Psoas Muscle	Psoas
31	chr2:73715000-73717600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:73715000-73717800	Weak transcription	Fetal Lung	lung
33	chr2:73715000-73719200	Strong transcription	Ovary	ovary
34	chr2:73715000-73719400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:73715000-73719800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:73715000-73719800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:73715000-73721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:73715000-73724600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:73715200-73717000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:73715200-73717000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:73715200-73717000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:73715200-73717800	Strong transcription	Fetal Stomach	stomach
43	chr2:73715200-73719000	Strong transcription	Dnd41	blood
44	chr2:73715200-73722600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:73715400-73717200	Weak transcription	Brain Germinal Matrix	brain
46	chr2:73715400-73717200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:73715400-73718200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:73715400-73719200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:73715400-73719200	Strong transcription	Fetal Brain Female	brain
50	chr2:73715400-73719600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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