Variant report

Variant	rs2900979
Chromosome Location	chr11:32850251-32850252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:32849868..32852880-chr11:32911360..32916794,6	MCF-7	breast:
2	chr11:32850001..32854483-chr11:32912810..32915962,5	MCF-7	breast:
3	chr11:32850121..32852277-chr11:33088797..33091531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000060749	Chromatin interaction
ENSG00000176148	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10835955	1.00[CEU][hapmap]
rs11031928	1.00[CEU][hapmap]
rs11031939	1.00[CEU][hapmap]
rs11031949	1.00[CEU][hapmap]
rs11031951	0.89[CEU][hapmap]
rs11031952	1.00[CEU][hapmap]
rs11031975	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11031978	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11031981	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11031994	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11031999	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11032000	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11032017	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11032026	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032043	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12365215	1.00[AFR][1000 genomes]
rs12365339	1.00[CEU][hapmap]
rs1396994	1.00[CEU][hapmap]
rs197702	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197703	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs197706	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs197708	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2143572	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179644	1.00[ASN][1000 genomes]
rs2419772	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419773	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664693	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2900980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34991296	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4755451	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4755455	0.80[EUR][1000 genomes]
rs4756328	0.80[EUR][1000 genomes]
rs7101848	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7109323	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7113870	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7124151	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761284	1.00[ASN][1000 genomes]
rs761285	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7931061	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935374	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7950261	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9943506	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2757434	chr11:32792784-32958609	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv34742	chr11:32796092-33004024	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv897190	chr11:32801921-32951836	Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv897191	chr11:32805169-32903263	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv897192	chr11:32828760-32903263	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv897193	chr11:32838288-32903263	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv825818	chr11:32849904-32852165	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2900979	PRRG4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32837400-32850800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:32843200-32850800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:32843800-32850600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:32844000-32850400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:32846400-32850400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:32846400-32850400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr11:32846600-32850400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:32846800-32850400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:32848200-32850400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:32849200-32850600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:32849400-32850800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:32850000-32850400	Enhancers	Hela-S3	cervix
13	chr11:32850000-32850400	Weak transcription	NHEK	skin
14	chr11:32850200-32850400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:32850200-32850400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:32850200-32850600	Enhancers	Liver	Liver
17	chr11:32850200-32850600	Enhancers	GM12878-XiMat	blood

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