Variant report

Variant	rs11883874
Chromosome Location	chr2:58317208-58317209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10164499	0.93[MKK][hapmap];0.84[YRI][hapmap]
rs10165760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10174202	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176681	0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176942	1.00[ASN][1000 genomes]
rs10178025	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10182762	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187411	0.87[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs10203014	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1025755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10518852	1.00[MKK][hapmap]
rs11891477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11892302	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900900	0.89[AMR][1000 genomes]
rs12104650	0.81[AFR][1000 genomes]
rs12105064	0.81[AMR][1000 genomes]
rs13382369	0.82[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13394820	0.95[AFR][1000 genomes]
rs13397947	0.89[AMR][1000 genomes]
rs13405281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13410228	0.82[AFR][1000 genomes]
rs13410500	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419989	0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13431271	0.82[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1371213	0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049333	1.00[ASN][1000 genomes]
rs17049337	1.00[ASN][1000 genomes]
rs17049338	1.00[ASN][1000 genomes]
rs17049343	1.00[GIH][hapmap]
rs17049345	1.00[GIH][hapmap]
rs17049414	1.00[ASN][1000 genomes]
rs2165100	0.82[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes]
rs2165103	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2312486	0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28521626	0.95[AFR][1000 genomes]
rs4459722	0.89[AFR][1000 genomes]
rs57112138	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57597086	0.83[AFR][1000 genomes]
rs58470176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60364084	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718190	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6740373	0.89[AMR][1000 genomes]
rs6740836	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6742445	0.89[AMR][1000 genomes]
rs716758	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948876	0.89[AMR][1000 genomes]
rs72949131	0.82[AFR][1000 genomes]
rs72949137	0.92[AFR][1000 genomes]
rs72951042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7340170	0.89[AMR][1000 genomes]
rs73944804	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7563225	0.96[MKK][hapmap]
rs7563312	0.84[AFR][1000 genomes]
rs7569184	0.81[AMR][1000 genomes]
rs7569731	0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs7574578	0.89[AMR][1000 genomes]
rs7574694	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7577402	1.00[ASN][1000 genomes]
rs7590976	1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[AMR][1000 genomes]
rs7597069	0.89[AMR][1000 genomes]
rs7600213	0.90[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes]
rs9309303	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs9973345	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9973928	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv527551	chr2:58311684-58317208	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58274800-58317400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:58275000-58317400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:58275000-58321600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
5	chr2:58279000-58319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:58284200-58317600	Weak transcription	HepG2	liver
8	chr2:58284400-58325000	Weak transcription	NHEK	skin
9	chr2:58286200-58317600	Weak transcription	K562	blood
10	chr2:58286400-58317600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:58291600-58317800	Weak transcription	HSMM	muscle
12	chr2:58291600-58317800	Weak transcription	NH-A	brain
13	chr2:58291600-58319000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:58291600-58321800	Weak transcription	Fetal Thymus	thymus
15	chr2:58291600-58325000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:58291800-58318800	Weak transcription	Osteobl	bone
17	chr2:58292200-58319000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:58292200-58319000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:58294200-58320800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:58297600-58319000	Weak transcription	Primary T cells from cord blood	blood
21	chr2:58298000-58317600	Weak transcription	Left Ventricle	heart
22	chr2:58301600-58319200	Weak transcription	Psoas Muscle	Psoas
23	chr2:58303000-58358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:58307600-58328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:58308600-58321600	Weak transcription	Lung	lung
26	chr2:58308600-58333600	Weak transcription	NHDF-Ad	bronchial
27	chr2:58309400-58324400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:58310400-58320200	Weak transcription	Small Intestine	intestine
29	chr2:58310400-58326000	Weak transcription	Hela-S3	cervix
30	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
31	chr2:58311400-58320000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:58312200-58317600	Weak transcription	Fetal Heart	heart
33	chr2:58312200-58322000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:58312200-58323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:58312800-58317600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:58313400-58319200	Strong transcription	Liver	Liver
37	chr2:58313600-58318400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:58313600-58320000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:58313800-58319000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:58313800-58320000	Strong transcription	Primary B cells from cord blood	blood
41	chr2:58314000-58317400	Weak transcription	Placenta	Placenta
42	chr2:58314200-58319800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:58314200-58322200	Weak transcription	NHLF	lung
44	chr2:58314400-58320200	Weak transcription	Colonic Mucosa	Colon
45	chr2:58314600-58317600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:58314600-58320000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:58314600-58320000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:58315200-58318200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:58315200-58319200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:58315200-58319800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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