Variant report

Variant	rs2608023
Chromosome Location	chr3:78771696-78771697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10865570	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11708898	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11714414	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11927671	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043662	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs2118067	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2164549	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2255164	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2684377	0.85[EUR][1000 genomes]
rs28429251	0.93[EUR][1000 genomes]
rs28482804	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56315536	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769521	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs6785152	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7619742	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs967454	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9834909	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9837496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984138	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs9842948	0.87[EUR][1000 genomes]
rs9856624	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes]
rs9864412	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9874934	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9875094	1.00[CEU][hapmap];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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv1842222	chr3:78744206-78778901	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78733800-78778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
4	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:78754000-78772200	Weak transcription	Brain Substantia Nigra	brain
7	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
8	chr3:78756800-78777800	Weak transcription	Osteobl	bone
9	chr3:78757200-78773800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:78762600-78772800	Weak transcription	Brain Anterior Caudate	brain
15	chr3:78762800-78774000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:78763000-78772600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:78763600-78773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:78764200-78777400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:78765800-78778000	Weak transcription	HMEC	breast
20	chr3:78766200-78773200	Weak transcription	Primary T cells from cord blood	blood
21	chr3:78766400-78772200	Weak transcription	Fetal Stomach	stomach
22	chr3:78766400-78774000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:78766400-78777400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:78766400-78778000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:78766400-78778000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:78766600-78773600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:78766600-78773800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:78766600-78773800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:78766600-78773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:78766600-78774200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:78766600-78774200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:78766600-78778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:78766600-78778000	Weak transcription	Ovary	ovary
34	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:78770400-78771800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:78771000-78772000	Enhancers	A549	lung
37	chr3:78771000-78774600	Enhancers	Fetal Lung	lung
38	chr3:78771200-78772000	Enhancers	Hela-S3	cervix
39	chr3:78771200-78774200	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:78771400-78772000	Enhancers	NHEK	skin
41	chr3:78771400-78772200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:78771400-78773600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:78771400-78773800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:78771600-78772000	Enhancers	HepG2	liver
45	chr3:78771600-78772800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:78771600-78774000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:78771600-78774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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