Variant report

Variant	rs540427
Chromosome Location	chr9:79146227-79146228
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79141157..79143063-chr9:79143309..79146258,3	MCF-7	breast:
2	chr9:79074092..79076244-chr9:79145228..79147118,2	MCF-7	breast:
3	chr9:79145810..79147846-chr9:79148207..79150771,2	MCF-7	breast:
4	chr9:79073112..79077050-chr9:79144085..79148483,6	MCF-7	breast:
5	chr9:79139489..79141014-chr9:79144768..79146907,2	MCF-7	breast:
6	chr9:79139154..79140841-chr9:79144087..79146483,2	MCF-7	breast:
7	chr9:79141616..79143870-chr9:79144001..79146355,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11144942	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11144944	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11144945	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1747626	0.88[ASN][1000 genomes]
rs4744794	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4745555	0.84[CHB][hapmap]
rs506579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs536644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570212	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs570705	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs571600	0.95[ASN][1000 genomes]
rs608289	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs631887	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs785900	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1050280	chr9:79133978-79160451	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2753141	chr9:79134434-79159993	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79129200-79152000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:79132400-79148000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:79134400-79150800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:79134600-79152000	Weak transcription	Pancreas	Pancrea
5	chr9:79137200-79173600	Weak transcription	Primary B cells from cord blood	blood
6	chr9:79137600-79152400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:79141600-79149200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:79144000-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:79145200-79146400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:79145200-79148000	Enhancers	Osteobl	bone
11	chr9:79145400-79146400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:79145400-79146400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:79145400-79146800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:79145600-79146400	Enhancers	NHLF	lung
15	chr9:79145800-79146400	Enhancers	Primary B cells from peripheral blood	blood
16	chr9:79145800-79146400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:79145800-79146400	Enhancers	NH-A	brain
18	chr9:79145800-79146600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:79145800-79146600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:79146000-79146400	Weak transcription	Fetal Intestine Small	intestine
21	chr9:79146000-79146400	Enhancers	GM12878-XiMat	blood
22	chr9:79146000-79146800	Enhancers	Stomach Mucosa	stomach
23	chr9:79146000-79148000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:79146000-79148000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:79146000-79148200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:79146000-79148200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr9:79146000-79149200	Weak transcription	Small Intestine	intestine
28	chr9:79146000-79152000	Weak transcription	HSMMtube	muscle
29	chr9:79146200-79146600	Enhancers	HSMM	muscle
30	chr9:79146200-79146600	Enhancers	NHDF-Ad	bronchial
31	chr9:79146200-79146800	Enhancers	Right Atrium	heart
32	chr9:79146200-79148000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:79146200-79148000	Enhancers	Muscle Satellite Cultured Cells	--

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