Variant report

Variant	rs6804234
Chromosome Location	chr3:79035305-79035306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:79033431..79035396-chr3:79066510..79068950,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11127638	0.86[EUR][1000 genomes]
rs11923198	0.86[EUR][1000 genomes]
rs12495750	0.86[EUR][1000 genomes]
rs13096526	1.00[EUR][1000 genomes]
rs1349023	0.86[EUR][1000 genomes]
rs1349024	0.86[EUR][1000 genomes]
rs1374883	0.86[EUR][1000 genomes]
rs1374885	1.00[EUR][1000 genomes]
rs1374886	1.00[EUR][1000 genomes]
rs1374887	0.86[EUR][1000 genomes]
rs1374888	0.86[EUR][1000 genomes]
rs1374889	0.86[EUR][1000 genomes]
rs1900663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1947154	0.86[EUR][1000 genomes]
rs2871747	0.86[EUR][1000 genomes]
rs4680946	1.00[EUR][1000 genomes]
rs6548603	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6548604	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6548605	1.00[EUR][1000 genomes]
rs6548606	1.00[EUR][1000 genomes]
rs6774082	0.86[EUR][1000 genomes]
rs6788693	0.86[EUR][1000 genomes]
rs6797152	0.86[EUR][1000 genomes]
rs7625043	1.00[EUR][1000 genomes]
rs7646169	0.86[EUR][1000 genomes]
rs9845900	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	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv520937	chr3:79025569-79039406	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 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	chr3:79022400-79041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:79023800-79037400	Weak transcription	A549	lung
3	chr3:79031200-79035600	Weak transcription	Fetal Brain Male	brain
4	chr3:79031400-79035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:79031400-79035600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:79031400-79035600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:79031600-79035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:79034600-79036600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr3:79034600-79037600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:79034800-79037000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:79035000-79035600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:79035000-79035600	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:79035000-79036200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:79035000-79036200	Enhancers	Brain Angular Gyrus	brain
15	chr3:79035000-79036600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:79035000-79036800	Enhancers	Brain Hippocampus Middle	brain
17	chr3:79035200-79035400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:79035200-79035400	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr3:79035200-79035600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:79035200-79035600	Active TSS	Fetal Lung	lung
21	chr3:79035200-79035800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:79035200-79035800	Enhancers	Brain Germinal Matrix	brain
23	chr3:79035200-79035800	Enhancers	HepG2	liver
24	chr3:79035200-79036000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr3:79035200-79036000	Enhancers	Osteobl	bone
26	chr3:79035200-79036200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:79035200-79036200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr3:79035200-79036600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:79035200-79036600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:79035200-79036600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:79035200-79037000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:79035200-79037000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr3:79035200-79037600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:79035200-79037600	Enhancers	Brain Substantia Nigra	brain
35	chr3:79035200-79038000	Enhancers	HUES64 Cell Line	embryonic stem cell

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