Variant report

Variant	rs848289
Chromosome Location	chr2:58391570-58391571
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58382472..58384235-chr2:58388859..58391605,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10172212	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10188070	0.89[CEU][hapmap]
rs10490251	0.94[JPT][hapmap]
rs1100190	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12477242	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12620940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12622856	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12713370	0.83[JPT][hapmap]
rs1518395	0.82[JPT][hapmap]
rs2043890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2118899	0.80[AMR][1000 genomes]
rs3771221	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3771224	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709203	0.89[YRI][hapmap]
rs72618694	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72618695	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72618696	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs848285	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs848286	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs848287	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs848288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848294	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs986512	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:58358200-58393800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
6	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:58359800-58392000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:58374400-58393400	Weak transcription	NHEK	skin
15	chr2:58374400-58397400	Weak transcription	Fetal Heart	heart
16	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
17	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:58381200-58391600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:58382200-58393200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:58382400-58391800	Strong transcription	Dnd41	blood
21	chr2:58382600-58394000	Weak transcription	Fetal Brain Male	brain
22	chr2:58382600-58395400	Weak transcription	Pancreas	Pancrea
23	chr2:58382600-58395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
25	chr2:58382600-58400400	Weak transcription	Gastric	stomach
26	chr2:58382800-58394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:58382800-58395800	Weak transcription	Lung	lung
28	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:58383200-58391800	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
34	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:58384000-58393800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:58384200-58392200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:58384200-58394800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:58384400-58391800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:58384400-58391800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:58384400-58392200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:58384600-58393000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:58384600-58393000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:58384600-58393000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:58384800-58395400	Weak transcription	Aorta	Aorta
45	chr2:58385000-58394600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
47	chr2:58385200-58398200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:58385200-58424600	Weak transcription	Ovary	ovary
49	chr2:58385400-58395600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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