Variant report

Variant	rs6439801
Chromosome Location	chr3:138041363-138041364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16847931	1.00[MEX][hapmap]
rs3886726	1.00[MEX][hapmap]
rs6439802	0.87[ASW][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes]
rs6789862	1.00[MEX][hapmap]
rs6790420	1.00[MEX][hapmap]
rs6790428	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs6796118	1.00[MEX][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv221877	chr3:138041360-138041363	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138018200-138042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:138026200-138042600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:138028800-138046600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:138034400-138042400	Weak transcription	NHEK	skin
5	chr3:138035600-138046800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:138037200-138042200	Weak transcription	Psoas Muscle	Psoas
7	chr3:138037600-138041600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:138038600-138048200	Weak transcription	Gastric	stomach
9	chr3:138039800-138042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:138040200-138041400	Weak transcription	Primary T cells from cord blood	blood
11	chr3:138040400-138041400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:138040400-138041800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:138040600-138041800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:138040800-138041600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:138040800-138041600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:138040800-138042200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:138041000-138041400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:138041000-138041800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:138041000-138043400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:138041200-138041600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:138041200-138041600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:138041200-138041800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:138041200-138041800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:138041200-138042000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr3:138041200-138042000	Enhancers	Fetal Thymus	thymus
26	chr3:138041200-138042400	Enhancers	Primary T cells fromperipheralblood	blood

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