Variant report

Variant	rs4909917
Chromosome Location	chr11:9981165-9981166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10500715	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10500717	0.80[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs10743123	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10770077	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10770078	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10770079	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10840327	0.86[CEU][hapmap]
rs10840330	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840333	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840334	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840337	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs10840338	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs10840347	0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10840348	0.80[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs10840359	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10840361	0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10840362	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10840370	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11042543	0.81[CEU][hapmap]
rs11042558	0.90[ASN][1000 genomes]
rs11042559	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs11042561	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs11042571	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs11042573	0.82[EUR][1000 genomes]
rs11042574	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11042578	0.88[EUR][1000 genomes]
rs11042579	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11042580	0.86[EUR][1000 genomes]
rs11042589	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11042590	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11042591	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11042595	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs11042601	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs11042604	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11042605	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11042609	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs11042613	0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs11042615	0.86[CEU][hapmap]
rs11042618	0.85[CEU][hapmap]
rs11042623	0.84[CEU][hapmap]
rs11042624	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11042632	0.89[CEU][hapmap]
rs11042639	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11042641	0.81[CEU][hapmap]
rs11042645	1.00[JPT][hapmap]
rs11600251	0.86[CEU][hapmap]
rs11602465	0.88[EUR][1000 genomes]
rs11602515	0.86[CEU][hapmap]
rs11603440	0.87[EUR][1000 genomes]
rs11606561	0.86[CEU][hapmap]
rs12222953	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12283105	1.00[JPT][hapmap]
rs12290996	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12417184	0.88[CEU][hapmap]
rs12419923	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs12420734	0.88[CEU][hapmap]
rs12420950	0.84[EUR][1000 genomes]
rs12421096	0.85[CEU][hapmap]
rs12421200	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs12575719	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs1372807	0.95[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs1442732	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs16907368	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs16907396	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs17271847	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs17356792	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2403226	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403227	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2403229	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4478985	0.81[EUR][1000 genomes]
rs4529876	0.82[EUR][1000 genomes]
rs4576815	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4625455	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4909915	0.86[CEU][hapmap]
rs4910080	0.82[CEU][hapmap]
rs4910081	0.86[CEU][hapmap]
rs4910086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58084362	0.88[ASN][1000 genomes]
rs60362241	0.88[ASN][1000 genomes]
rs7106914	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs7114044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7114303	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs7123453	0.85[CEU][hapmap]
rs7131445	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7928959	0.86[CEU][hapmap]
rs7933475	0.96[ASN][1000 genomes]
rs7938491	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs7938502	0.86[CEU][hapmap]
rs7938647	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs7938788	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7946995	0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs7950447	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs7951950	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv982983	chr11:9980342-9981342	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4909917	OR5E1P	cis	parietal	SCAN
rs4909917	ZNF143	cis	cerebellum	SCAN
rs4909917	OR10A5	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9968000-9984000	Weak transcription	Primary B cells from cord blood	blood
3	chr11:9968000-9984200	Weak transcription	Fetal Kidney	kidney
4	chr11:9973000-9986000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
6	chr11:9974200-9994400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:9974200-9994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:9974200-9994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
10	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
11	chr11:9974400-9982800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:9975400-9985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:9977000-9994400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:9977600-9982000	Weak transcription	Stomach Mucosa	stomach
15	chr11:9977800-9981600	Strong transcription	Fetal Lung	lung
16	chr11:9978200-9981600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:9978600-9981800	Strong transcription	Left Ventricle	heart
18	chr11:9978600-9986000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:9978800-9985000	Weak transcription	Small Intestine	intestine
20	chr11:9979400-9981600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:9979400-9982000	Weak transcription	Colonic Mucosa	Colon
22	chr11:9979400-9986000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:9979400-9995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:9979600-9981600	Strong transcription	Fetal Muscle Leg	muscle
25	chr11:9979600-9981800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:9979600-9982000	Strong transcription	Fetal Stomach	stomach
27	chr11:9979600-9985600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:9979600-9985800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:9979600-9994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:9979800-9981200	Weak transcription	Lung	lung
31	chr11:9979800-9987400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:9979800-9999200	Weak transcription	NH-A	brain
33	chr11:9980000-9981600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:9980000-9982200	Weak transcription	Thymus	Thymus
35	chr11:9980200-9981200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:9980200-9981200	Strong transcription	NHDF-Ad	bronchial
37	chr11:9980200-9981200	Strong transcription	Osteobl	bone
38	chr11:9980200-9981400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:9980200-9981400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:9980200-9981400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:9980200-9981400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr11:9980200-9981400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:9980200-9981400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:9980200-9981400	Strong transcription	Aorta	Aorta
45	chr11:9980200-9981400	Strong transcription	Colon Smooth Muscle	Colon
46	chr11:9980200-9981400	Strong transcription	Fetal Intestine Large	intestine
47	chr11:9980200-9981400	Strong transcription	Fetal Intestine Small	intestine
48	chr11:9980200-9981400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr11:9980200-9981400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr11:9980200-9981400	Strong transcription	Right Ventricle	heart

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