Variant report

Variant	rs2581928
Chromosome Location	chr11:57202790-57202791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11229028	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11820985	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11822095	0.96[ASN][1000 genomes]
rs11822910	0.98[ASN][1000 genomes]
rs11827928	0.98[ASN][1000 genomes]
rs11828218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12422015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12788236	0.81[ASN][1000 genomes]
rs2250887	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439448	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2467333	0.81[EUR][1000 genomes]
rs2511982	0.85[EUR][1000 genomes]
rs2581924	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2581927	0.87[EUR][1000 genomes]
rs2584858	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729389	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729392	0.87[EUR][1000 genomes]
rs4477456	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4529894	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60961847	0.91[ASN][1000 genomes]
rs61886978	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7106223	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7122734	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7943531	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2581928	SLC43A3	cis	cerebellum	SCAN
rs2581928	OR5T3	cis	parietal	SCAN
rs2581928	OR5AR1	cis	parietal	SCAN
rs2581928	TIMM10	cis	parietal	SCAN
rs2581928	OR8U1	cis	cerebellum	SCAN
rs2581928	SLC43A1	cis	cerebellum	SCAN
rs2581928	OR5AP2	cis	parietal	SCAN
rs2581928	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2581928	DTX4	cis	cerebellum	SCAN
rs2581928	TIMM10	cis	cerebellum	SCAN
rs2581928	OR5M8	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57197000-57203000	Enhancers	HepG2	liver
2	chr11:57198200-57202800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:57198400-57203000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:57199200-57203800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:57199400-57202800	Enhancers	Adipose Nuclei	Adipose
6	chr11:57199400-57203000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:57199400-57203000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:57199400-57203000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:57199400-57203000	Enhancers	Osteobl	bone
10	chr11:57199600-57203000	Enhancers	HMEC	breast
11	chr11:57199600-57203000	Enhancers	NHDF-Ad	bronchial
12	chr11:57199800-57203000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:57199800-57203000	Enhancers	NHLF	lung
14	chr11:57200000-57205600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:57200400-57202800	Enhancers	K562	blood
16	chr11:57200400-57203000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:57200400-57203000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr11:57200400-57203000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:57200400-57208000	Weak transcription	Lung	lung
20	chr11:57200800-57203000	Enhancers	Hela-S3	cervix
21	chr11:57201400-57203000	Enhancers	Fetal Lung	lung
22	chr11:57201600-57202800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr11:57201600-57202800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:57201600-57203000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr11:57201600-57203000	Enhancers	Fetal Intestine Small	intestine
26	chr11:57201800-57202800	Enhancers	Colon Smooth Muscle	Colon
27	chr11:57201800-57202800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr11:57201800-57203000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr11:57201800-57203000	Enhancers	Fetal Intestine Large	intestine
30	chr11:57202000-57202800	Enhancers	Stomach Smooth Muscle	stomach
31	chr11:57202000-57202800	Enhancers	HSMM	muscle
32	chr11:57202000-57203000	Enhancers	NHEK	skin
33	chr11:57202000-57210200	Enhancers	Liver	Liver
34	chr11:57202200-57202800	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:57202200-57203000	Enhancers	Rectal Smooth Muscle	rectum
36	chr11:57202400-57202800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:57202400-57202800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr11:57202400-57202800	Enhancers	Esophagus	oesophagus
39	chr11:57202400-57202800	Enhancers	Placenta	Placenta
40	chr11:57202400-57202800	Enhancers	Pancreas	Pancrea
41	chr11:57202400-57203000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr11:57202600-57202800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr11:57202600-57202800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr11:57202600-57203000	Enhancers	Right Atrium	heart
45	chr11:57202600-57203800	Enhancers	A549	lung

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