Variant report

Variant	rs1855142
Chromosome Location	chr9:14904759-14904760
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	chr9:14897379..14899021-chr9:14903144..14904953,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10122340	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs10961784	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs10961785	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1412725	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1916314	0.81[MKK][hapmap]
rs2030594	0.81[AMR][1000 genomes]
rs4147129	0.87[CHB][hapmap]
rs4543641	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs6474870	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6474872	0.83[AMR][1000 genomes]
rs7034380	0.87[CHB][hapmap];0.81[GIH][hapmap]
rs7848497	0.86[MEX][hapmap];0.83[MKK][hapmap]
rs7861117	0.89[ASW][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs940119	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs940120	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831518	chr9:14760638-14953501	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1018416	chr9:14846753-14921247	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1855142	FREM1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14884200-14907400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr9:14895200-14906200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:14900000-14906200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:14900200-14906600	Weak transcription	Adipose Nuclei	Adipose
5	chr9:14900200-14906600	Weak transcription	Aorta	Aorta
6	chr9:14902200-14905000	Genic enhancers	Fetal Kidney	kidney
7	chr9:14902200-14906000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:14902400-14906200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:14902600-14906200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:14902600-14906600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:14902600-14906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:14902600-14906600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:14902800-14904800	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:14902800-14906400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:14902800-14906400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:14902800-14906600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:14903000-14906000	Weak transcription	Fetal Heart	heart
18	chr9:14903200-14908600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:14903400-14905800	Weak transcription	Fetal Stomach	stomach
20	chr9:14903600-14906400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:14903600-14906400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:14904400-14904800	Enhancers	Fetal Lung	lung
23	chr9:14904400-14905200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:14904400-14907200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr9:14904600-14904800	Enhancers	Rectal Smooth Muscle	rectum
26	chr9:14904600-14906000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:14904600-14906000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:14904600-14906200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:14904600-14906400	Enhancers	Colon Smooth Muscle	Colon
30	chr9:14904600-14907400	Enhancers	HepG2	liver
31	chr9:14904600-14907600	Enhancers	Pancreas	Pancrea

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