Variant report

Variant	rs9839459
Chromosome Location	chr3:78761628-78761629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10049016	1.00[EUR][1000 genomes]
rs28497208	1.00[EUR][1000 genomes]
rs3773204	1.00[EUR][1000 genomes]
rs3821594	1.00[EUR][1000 genomes]
rs6774609	1.00[EUR][1000 genomes]
rs72908874	1.00[EUR][1000 genomes]
rs7642059	1.00[EUR][1000 genomes]
rs9828832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9851220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9862358	1.00[EUR][1000 genomes]
rs9864178	1.00[EUR][1000 genomes]
rs9866063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:35 , 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	chr3:78735200-78765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
5	chr3:78749000-78765800	Weak transcription	Ovary	ovary
6	chr3:78749600-78765600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:78752600-78771000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:78753200-78765800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:78753600-78762400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:78754000-78762400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:78754000-78765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:78754000-78772200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:78756200-78765800	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
17	chr3:78756800-78762200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:78756800-78777800	Weak transcription	Osteobl	bone
19	chr3:78757000-78762000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:78757000-78765600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:78757000-78771000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:78757200-78762600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:78757200-78765400	Weak transcription	Fetal Stomach	stomach
24	chr3:78757200-78765800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:78757200-78768400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:78757200-78773800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:78757400-78762600	Weak transcription	Fetal Lung	lung
29	chr3:78758600-78765800	Weak transcription	HepG2	liver
30	chr3:78761000-78762800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:78761200-78765800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:78761400-78763200	Enhancers	Primary T cells from cord blood	blood
34	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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