Variant report

Variant	rs13424099
Chromosome Location	chr2:58322052-58322053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10167028	0.91[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10179025	0.86[AFR][1000 genomes]
rs10184957	1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs10185542	0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs10185758	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10198382	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10203887	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903212	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs12624152	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs13001078	0.91[CEU][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13006005	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs13008111	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13023405	0.91[CEU][hapmap]
rs13033987	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384786	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13386998	0.83[CEU][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13392156	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13402655	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409706	0.89[AFR][1000 genomes]
rs13414973	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13417865	0.84[AFR][1000 genomes]
rs13418777	0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs13421853	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs13424848	0.85[YRI][hapmap]
rs13428078	0.86[AFR][1000 genomes]
rs13430450	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1404457	0.91[CEU][hapmap]
rs1404460	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs17182870	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17183100	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28391566	0.86[AFR][1000 genomes]
rs28452374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28668929	0.81[AFR][1000 genomes]
rs34287580	0.92[EUR][1000 genomes]
rs35341336	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755296	0.88[CEU][hapmap]
rs3771214	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3771220	0.83[CEU][hapmap]
rs3771222	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs6714952	0.83[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs71418479	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71418480	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558066	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs7561771	0.91[CEU][hapmap]

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	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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
2	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:58284400-58325000	Weak transcription	NHEK	skin
4	chr2:58291600-58325000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:58303000-58358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:58307600-58328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:58308600-58333600	Weak transcription	NHDF-Ad	bronchial
8	chr2:58309400-58324400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:58310400-58326000	Weak transcription	Hela-S3	cervix
10	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
11	chr2:58312200-58323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:58314200-58322200	Weak transcription	NHLF	lung
13	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:58316000-58323000	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:58316400-58322800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:58316600-58326200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:58318200-58327600	Weak transcription	Placenta	Placenta
18	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:58318400-58334800	Weak transcription	HSMM	muscle
20	chr2:58318800-58325400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:58319400-58358400	Weak transcription	Ovary	ovary
22	chr2:58319600-58323600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:58319600-58326600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:58319800-58322400	Weak transcription	NH-A	brain
25	chr2:58319800-58322800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:58319800-58322800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:58319800-58325000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:58319800-58325000	Weak transcription	HMEC	breast
29	chr2:58319800-58325400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:58319800-58325400	Weak transcription	Osteobl	bone
31	chr2:58319800-58326000	Weak transcription	K562	blood
32	chr2:58319800-58326200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
34	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:58320000-58322200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:58320000-58322400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:58320000-58322400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:58320000-58322400	Weak transcription	Adipose Nuclei	Adipose
41	chr2:58320000-58325000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:58320000-58325000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:58320000-58325200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:58320000-58326400	Weak transcription	Primary B cells from cord blood	blood
45	chr2:58320000-58326600	Weak transcription	Psoas Muscle	Psoas
46	chr2:58320000-58327600	Weak transcription	Fetal Lung	lung
47	chr2:58320000-58334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:58320000-58334600	Weak transcription	HUVEC	blood vessel
49	chr2:58320000-58334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:58320000-58339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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