Variant report

Variant	rs848291
Chromosome Location	chr2:58388696-58388697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1016771	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1051061	1.00[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1100188	0.87[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1100191	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11678320	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12622856	1.00[YRI][hapmap]
rs12996679	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs12999901	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13011711	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691672	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35248619	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732136	0.83[LWK][hapmap]
rs3771213	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57390191	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62140014	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709460	0.85[AFR][1000 genomes]
rs6727746	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6761301	0.84[LWK][hapmap]
rs7561688	0.90[MEX][hapmap]
rs848278	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs848279	0.87[CEU][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs848280	0.83[CEU][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs848281	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs848282	0.83[CEU][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs848284	0.81[EUR][1000 genomes]
rs848292	0.87[CEU][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:58358200-58393800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:58358400-58389000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:58359000-58391400	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
9	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:58359400-58389400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:58359800-58392000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:58365200-58390000	Weak transcription	Psoas Muscle	Psoas
15	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:58373800-58389600	Weak transcription	Thymus	Thymus
20	chr2:58374000-58389400	Weak transcription	Right Ventricle	heart
21	chr2:58374400-58393400	Weak transcription	NHEK	skin
22	chr2:58374400-58397400	Weak transcription	Fetal Heart	heart
23	chr2:58379800-58389400	Strong transcription	Primary B cells from cord blood	blood
24	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
25	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:58381200-58391600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:58381800-58390000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:58382200-58388800	Strong transcription	GM12878-XiMat	blood
29	chr2:58382200-58390200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:58382200-58393200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:58382400-58389200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:58382400-58390000	Strong transcription	Adipose Nuclei	Adipose
33	chr2:58382400-58390200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:58382400-58390400	Strong transcription	Fetal Intestine Large	intestine
35	chr2:58382400-58391800	Strong transcription	Dnd41	blood
36	chr2:58382600-58390600	Strong transcription	Liver	Liver
37	chr2:58382600-58391400	Weak transcription	Brain Angular Gyrus	brain
38	chr2:58382600-58394000	Weak transcription	Fetal Brain Male	brain
39	chr2:58382600-58395400	Weak transcription	Pancreas	Pancrea
40	chr2:58382600-58395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
42	chr2:58382600-58400400	Weak transcription	Gastric	stomach
43	chr2:58382800-58394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:58382800-58395800	Weak transcription	Lung	lung
45	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:58383200-58389600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:58383200-58391800	Weak transcription	Colon Smooth Muscle	Colon

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