Variant report

Variant	rs4292454
Chromosome Location	chr5:42623245-42623246
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	chr5:42491642..42494093-chr5:42621929..42623972,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10041108	1.00[CHB][hapmap]
rs10440649	1.00[CHB][hapmap]
rs11957404	1.00[CHB][hapmap]
rs13156541	1.00[CHB][hapmap]
rs13168440	1.00[CHB][hapmap]
rs13171720	1.00[CHB][hapmap]
rs13182117	1.00[CHB][hapmap]
rs13184352	1.00[CHB][hapmap]
rs13188386	1.00[CHB][hapmap]
rs13354167	1.00[CHB][hapmap]
rs17574527	1.00[CHB][hapmap]
rs17574616	1.00[CHB][hapmap]
rs17575164	1.00[CHB][hapmap]
rs17636762	1.00[CHB][hapmap]
rs28943882	1.00[CHB][hapmap]
rs4129472	1.00[CHB][hapmap]
rs5025611	1.00[CHB][hapmap]
rs6413428	1.00[CHB][hapmap]
rs6414898	1.00[CHB][hapmap]
rs6451634	1.00[CHB][hapmap]
rs6451641	1.00[CHB][hapmap]
rs6451643	1.00[CHB][hapmap]
rs6863381	1.00[CHB][hapmap]
rs6873340	1.00[CHB][hapmap]
rs7444761	1.00[CHB][hapmap]
rs7702524	1.00[CHB][hapmap]
rs7703669	1.00[CHB][hapmap]
rs7709790	1.00[CHB][hapmap]
rs7718962	1.00[CHB][hapmap]
rs9292854	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1027023	chr5:42610250-42654999	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1019648	chr5:42616487-42696943	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv537736	chr5:42616487-42696943	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv1810677	chr5:42623245-42630968	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4292454	GHR	cis	brain	BrainEAC
rs4292454	GHR	cis	temporal cortex	BrainEAC

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42610800-42626800	Weak transcription	Pancreas	Pancrea
2	chr5:42615600-42626200	Weak transcription	Aorta	Aorta
3	chr5:42619600-42624200	Genic enhancers	Liver	Liver
4	chr5:42619600-42624400	Enhancers	Primary B cells from peripheral blood	blood
5	chr5:42621200-42624000	Enhancers	Psoas Muscle	Psoas
6	chr5:42621800-42626200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:42621800-42629000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:42622200-42623800	Enhancers	Primary B cells from cord blood	blood
9	chr5:42622400-42623600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:42622400-42624200	Weak transcription	Fetal Lung	lung
11	chr5:42622600-42626800	Weak transcription	Ovary	ovary
12	chr5:42622600-42626800	Weak transcription	Right Ventricle	heart
13	chr5:42622600-42627800	Weak transcription	Left Ventricle	heart
14	chr5:42622600-42628800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:42622800-42624000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:42622800-42631200	Weak transcription	Adipose Nuclei	Adipose
17	chr5:42623000-42626200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:42623000-42626600	Weak transcription	Fetal Heart	heart
19	chr5:42623000-42631400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:42623000-42644400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:42623200-42623600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:42623200-42624200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:42623200-42631400	Weak transcription	Right Atrium	heart

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