Variant report

Variant	rs416025
Chromosome Location	chr3:78804034-78804035
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:13)

rs_ID	r²[population]
rs11127633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716325	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs12636958	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13083478	0.81[ASN][1000 genomes]
rs1386431	0.87[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1865862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608021	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs333472	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs34811803	0.95[ASN][1000 genomes]
rs3926199	0.89[ASN][1000 genomes]
rs424737	0.84[ASN][1000 genomes]
rs444992	0.84[ASN][1000 genomes]
rs57373402	0.84[ASN][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	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
3	esv2753211	chr3:78784269-78809116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78787400-78814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:78798600-78810200	Weak transcription	Fetal Lung	lung
3	chr3:78802200-78810200	Weak transcription	Fetal Stomach	stomach
4	chr3:78802400-78804200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:78802400-78804200	Enhancers	HMEC	breast
6	chr3:78802400-78804400	Enhancers	Hela-S3	cervix
7	chr3:78802400-78804600	Enhancers	Brain Angular Gyrus	brain
8	chr3:78802600-78804200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:78802600-78804600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:78802800-78804200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:78803200-78804200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:78803200-78804600	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:78803200-78804800	Enhancers	HepG2	liver
14	chr3:78803400-78804600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:78803400-78804600	Enhancers	Fetal Muscle Leg	muscle
16	chr3:78803400-78806600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:78803600-78804600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:78803600-78805800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:78803800-78804800	Enhancers	Brain Hippocampus Middle	brain
20	chr3:78803800-78806800	Weak transcription	Brain Germinal Matrix	brain
21	chr3:78803800-78814800	Weak transcription	NHDF-Ad	bronchial
22	chr3:78804000-78804200	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr3:78804000-78804400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:78804000-78804400	Active TSS	Spleen	Spleen
25	chr3:78804000-78804600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:78804000-78804600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:78804000-78804600	Enhancers	Pancreas	Pancrea
28	chr3:78804000-78804800	Enhancers	Brain Anterior Caudate	brain
29	chr3:78804000-78804800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:78804000-78805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:78804000-78806400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:78804000-78806400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:78804000-78806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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