Variant report

Variant	rs11228985
Chromosome Location	chr11:57048184-57048185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10501367	0.82[GIH][hapmap]
rs10792083	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs10792085	0.84[CEU][hapmap]
rs10896595	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896597	0.92[ASN][1000 genomes]
rs10896599	0.89[ASN][1000 genomes]
rs10896602	0.84[CEU][hapmap]
rs11228968	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228975	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228976	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228978	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228980	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228982	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11228984	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11228988	0.87[EUR][1000 genomes]
rs11544374	0.82[GIH][hapmap]
rs11600878	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604373	0.83[EUR][1000 genomes]
rs11604560	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604778	0.86[ASN][1000 genomes]
rs11605053	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607817	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419065	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12421633	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421755	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12792781	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs12797769	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17572970	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17651610	0.97[ASN][1000 genomes]
rs17652078	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892963	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892964	0.92[ASN][1000 genomes]
rs1939489	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939495	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2155230	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2155231	0.87[ASN][1000 genomes]
rs2226613	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276038	0.82[JPT][hapmap]
rs2511026	0.83[ASN][1000 genomes]
rs2511029	0.87[ASN][1000 genomes]
rs2511030	0.92[ASN][1000 genomes]
rs2846042	0.92[ASN][1000 genomes]
rs2846050	0.92[ASN][1000 genomes]
rs2846051	0.85[ASN][1000 genomes]
rs2851722	0.92[ASN][1000 genomes]
rs35610294	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3935068	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4384399	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4565915	0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs479949	0.92[ASN][1000 genomes]
rs4938855	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938857	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938859	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4938861	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4939132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs499318	0.91[ASN][1000 genomes]
rs5012051	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs519277	0.92[ASN][1000 genomes]
rs522656	0.87[ASN][1000 genomes]
rs528101	0.92[ASN][1000 genomes]
rs58295319	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs590240	0.87[ASN][1000 genomes]
rs599947	0.87[ASN][1000 genomes]
rs625565	0.92[ASN][1000 genomes]
rs652016	0.89[ASN][1000 genomes]
rs654635	0.92[ASN][1000 genomes]
rs6591413	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6591415	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6591416	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6591417	0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7102963	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119375	0.82[GIH][hapmap]
rs7120644	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7128371	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7130252	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72921992	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935236	0.94[ASN][1000 genomes]
rs7943761	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11228985	OR5AN1	cis	parietal	SCAN
rs11228985	GLYATL2	cis	parietal	SCAN
rs11228985	OR5T1	cis	cerebellum	SCAN
rs11228985	OR4C6	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57044200-57049000	Enhancers	Placenta	Placenta
2	chr11:57044800-57048400	Enhancers	HMEC	breast
3	chr11:57045000-57048200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:57045000-57048200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:57045000-57048200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:57045400-57048200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:57045800-57048200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:57045800-57048200	Enhancers	HSMM	muscle
9	chr11:57045800-57048200	Enhancers	NHEK	skin
10	chr11:57045800-57048200	Enhancers	NHLF	lung
11	chr11:57045800-57048200	Enhancers	Osteobl	bone
12	chr11:57045800-57048400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:57045800-57048400	Enhancers	NHDF-Ad	bronchial
14	chr11:57045800-57050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:57045800-57050600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:57045800-57051000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:57045800-57051200	Weak transcription	Esophagus	oesophagus
18	chr11:57045800-57054200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:57046000-57051000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:57046000-57062000	Weak transcription	Right Atrium	heart
21	chr11:57046200-57051000	Weak transcription	Small Intestine	intestine
22	chr11:57046200-57051000	Weak transcription	Stomach Mucosa	stomach
23	chr11:57046400-57050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:57046600-57050400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:57046600-57050400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:57046600-57050400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:57046600-57050600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:57046600-57056000	Weak transcription	Adipose Nuclei	Adipose
29	chr11:57046800-57048400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:57046800-57050600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:57046800-57051000	Weak transcription	HSMMtube	muscle
32	chr11:57046800-57051400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:57047000-57051000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr11:57047600-57048200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr11:57047600-57051200	Weak transcription	Hela-S3	cervix
36	chr11:57047800-57048200	Enhancers	Gastric	stomach
37	chr11:57048000-57048200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:57048000-57048200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr11:57048000-57050400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:57048000-57051200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:57048000-57051200	Weak transcription	Fetal Intestine Large	intestine

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