Variant report

Variant	rs2055439
Chromosome Location	chr5:75475258-75475259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75011937..75013471-chr5:75474552..75477211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152359	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1002541	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap]
rs10039662	0.98[ASN][1000 genomes]
rs10040232	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs10043982	0.90[EUR][1000 genomes]
rs10064352	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs10474464	0.92[YRI][hapmap]
rs10514062	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12152728	0.92[YRI][hapmap]
rs12153396	0.89[CHB][hapmap];0.84[CHD][hapmap]
rs12655684	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12657276	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs1393224	1.00[JPT][hapmap]
rs1423106	0.83[CHD][hapmap]
rs1423107	0.80[CHB][hapmap];0.84[CHD][hapmap]
rs1553325	0.92[YRI][hapmap]
rs17651115	0.93[GIH][hapmap]
rs17651269	0.90[CHB][hapmap]
rs2194177	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs2358531	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34476924	0.86[EUR][1000 genomes]
rs4493648	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704283	0.80[ASW][hapmap]
rs4704286	1.00[ASN][1000 genomes]
rs6414966	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414969	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6453206	0.91[GIH][hapmap]
rs6453208	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6868505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445798	0.98[ASN][1000 genomes]
rs7448148	0.98[ASN][1000 genomes]
rs7733832	0.90[EUR][1000 genomes]
rs9293675	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2055439	AGGF1	cis	parietal	SCAN
rs2055439	ORM1	trans	parietal	SCAN
rs2055439	FCHO2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75470600-75476400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:75471800-75477000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:75472400-75477000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:75472600-75475800	Enhancers	GM12878-XiMat	blood
5	chr5:75472600-75476200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:75472600-75476800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:75472600-75477000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:75472600-75477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:75472800-75476400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:75472800-75476600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:75472800-75476600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:75472800-75476800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:75472800-75477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:75473200-75475400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr5:75474000-75475400	Weak transcription	Placenta	Placenta
16	chr5:75474200-75475400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:75474200-75475400	Weak transcription	K562	blood
18	chr5:75474200-75475400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:75474200-75476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:75475000-75476200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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