Variant report

Variant	rs11685372
Chromosome Location	chr2:73749461-73749462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 155 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap]
rs10189578	0.81[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10192125	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10197233	0.85[EUR][1000 genomes]
rs1052161	0.87[JPT][hapmap]
rs1083919	0.80[ASN][1000 genomes]
rs1083920	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1083922	0.84[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1091568	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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]
rs11688718	0.93[ASN][1000 genomes]
rs11689767	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151671	0.86[EUR][1000 genomes]
rs1246094	0.83[ASN][1000 genomes]
rs1246096	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1246105	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs12478871	0.85[CEU][hapmap]
rs12618600	0.92[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs12620018	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12620091	0.82[CHB][hapmap]
rs12620569	0.86[EUR][1000 genomes]
rs12713783	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13007306	0.85[EUR][1000 genomes]
rs13007623	0.86[EUR][1000 genomes]
rs13017182	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs1320374	0.87[JPT][hapmap]
rs1403412	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1406105	0.81[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17349804	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1852645	0.85[AMR][1000 genomes];0.93[EUR][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]
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];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1881248	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2017116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2037814	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2056486	0.83[LWK][hapmap]
rs2280506	0.81[ASW][hapmap];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]
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];0.85[CHD][hapmap]
rs2421669	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2461691	0.85[EUR][1000 genomes]
rs28708576	0.82[EUR][1000 genomes]
rs2948441	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2950770	0.98[EUR][1000 genomes]
rs34719281	0.86[EUR][1000 genomes]
rs3820700	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3980696	0.83[EUR][1000 genomes]
rs4241256	0.86[EUR][1000 genomes]
rs4436991	0.82[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];0.80[AFR][1000 genomes];0.85[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	0.93[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	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054150	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56068325	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56770679	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153184	0.88[ASN][1000 genomes]
rs6546826	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs6546827	0.92[CHB][hapmap]
rs6546829	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6546830	0.86[EUR][1000 genomes]
rs6546831	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6546832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6546833	0.90[EUR][1000 genomes]
rs6546834	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6546838	0.87[LWK][hapmap]
rs6546842	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546846	0.86[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	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6706235	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.88[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	0.91[ASN][1000 genomes]
rs6732440	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6734450	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6742619	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6743576	0.87[ASN][1000 genomes]
rs6744273	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6744697	0.90[ASN][1000 genomes]
rs6745560	0.84[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap]
rs6746458	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs6749680	0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs6757996	0.93[ASN][1000 genomes]
rs6759464	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67877078	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67898050	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68154245	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72811933	0.85[ASN][1000 genomes]
rs72811939	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562047	0.83[ASN][1000 genomes]
rs7566315	0.90[ASN][1000 genomes]
rs7570014	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7574291	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs7576824	1.00[CHB][hapmap];0.88[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	0.83[ASN][1000 genomes]
rs7585668	0.85[EUR][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs7606483	0.82[ASN][1000 genomes]
rs7607989	0.81[ASW][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs7608308	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7609034	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7609249	0.87[ASN][1000 genomes]
rs780388	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780389	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780390	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780391	0.82[ASN][1000 genomes]
rs780393	0.82[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs802113	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11685372	ALMS1P	cis	cerebellum	SCAN
rs11685372	DUSP11	cis	parietal	SCAN
rs11685372	ALMS1P	cis	parietal	SCAN
rs11685372	DUSP11	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:73731600-73759000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:73731800-73752000	Weak transcription	Fetal Heart	heart
6	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
7	chr2:73736400-73761600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:73737600-73750600	Weak transcription	Small Intestine	intestine
9	chr2:73738800-73750200	Weak transcription	Stomach Mucosa	stomach
10	chr2:73739400-73756400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:73740800-73752600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:73740800-73752800	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:73740800-73753800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:73740800-73757600	Weak transcription	Ovary	ovary
15	chr2:73741000-73750200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:73741000-73751000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:73741000-73751800	Weak transcription	Fetal Kidney	kidney
18	chr2:73741000-73752200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:73741000-73752200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:73741000-73752200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:73741000-73752600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:73741000-73755000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:73741000-73755600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:73741000-73756200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:73741000-73756400	Weak transcription	Thymus	Thymus
26	chr2:73741000-73757200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:73741000-73757400	Weak transcription	Aorta	Aorta
28	chr2:73741000-73757400	Weak transcription	Pancreas	Pancrea
29	chr2:73741000-73757600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:73741000-73757800	Weak transcription	Gastric	stomach
31	chr2:73741000-73758800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:73741000-73759400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:73741000-73767400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:73741200-73751600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:73741200-73751800	Weak transcription	Brain Germinal Matrix	brain
36	chr2:73741200-73751800	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:73741200-73752000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:73741200-73752000	Weak transcription	Primary B cells from cord blood	blood
39	chr2:73741200-73752000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:73741200-73752400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:73741200-73757400	Weak transcription	Fetal Stomach	stomach
42	chr2:73741200-73757600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:73743600-73751200	Weak transcription	Fetal Intestine Large	intestine
44	chr2:73744200-73759000	Weak transcription	HSMMtube	muscle
45	chr2:73744200-73799800	Weak transcription	NH-A	brain
46	chr2:73744600-73750600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:73744600-73751800	Weak transcription	Fetal Brain Female	brain
48	chr2:73744600-73764400	Weak transcription	HSMM	muscle
49	chr2:73744800-73756600	Weak transcription	Fetal Brain Male	brain
50	chr2:73745200-73752000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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