Variant report

Variant	rs6548603
Chromosome Location	chr3:79033747-79033748
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:79026994..79029043-chr3:79031085..79033915,2	MCF-7	breast:
2	chr3:79033431..79035396-chr3:79066510..79068950,2	MCF-7	breast:
3	chr3:79031147..79033864-chr3:79073232..79075055,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11127638	1.00[EUR][1000 genomes]
rs11923198	1.00[EUR][1000 genomes]
rs12495750	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13096526	1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1349022	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1349023	1.00[EUR][1000 genomes]
rs1349024	1.00[EUR][1000 genomes]
rs1374883	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1374885	0.86[EUR][1000 genomes]
rs1374886	0.86[EUR][1000 genomes]
rs1374887	1.00[EUR][1000 genomes]
rs1374888	1.00[EUR][1000 genomes]
rs1374889	1.00[EUR][1000 genomes]
rs1550930	1.00[CHD][hapmap]
rs1900663	0.86[EUR][1000 genomes]
rs1947154	1.00[EUR][1000 genomes]
rs2871747	1.00[EUR][1000 genomes]
rs4680946	0.86[EUR][1000 genomes]
rs61586777	0.86[EUR][1000 genomes]
rs6548604	0.86[EUR][1000 genomes]
rs6548605	0.86[EUR][1000 genomes]
rs6548606	0.86[EUR][1000 genomes]
rs6774082	1.00[EUR][1000 genomes]
rs6788693	1.00[EUR][1000 genomes]
rs6795076	1.00[CHD][hapmap]
rs6797152	1.00[EUR][1000 genomes]
rs6804234	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7625043	0.86[EUR][1000 genomes]
rs7646169	1.00[EUR][1000 genomes]
rs9845900	1.00[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:26 , 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	chr3:79024800-79034600	Weak transcription	Fetal Lung	lung
4	chr3:79028400-79035200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:79028400-79035200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:79028800-79035000	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:79029000-79034600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:79029000-79035200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:79029000-79035200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:79029200-79034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:79029200-79035200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:79031200-79034800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:79031200-79035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:79031200-79035600	Weak transcription	Fetal Brain Male	brain
15	chr3:79031400-79035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:79031400-79035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:79031400-79035600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:79031400-79035600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:79031600-79035200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:79031600-79035200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:79031600-79035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:79031800-79035200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:79031800-79035200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:79033200-79035200	Weak transcription	HepG2	liver
25	chr3:79033400-79033800	Enhancers	Brain Anterior Caudate	brain
26	chr3:79033600-79033800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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