Variant report

Variant	rs1874109
Chromosome Location	chr9:14770580-14770581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10733289	0.84[CEU][hapmap]
rs13294910	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs13296345	0.80[CEU][hapmap];0.80[TSI][hapmap]
rs1494348	0.92[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs17218712	0.87[CEU][hapmap]
rs17218879	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1994919	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34882821	0.80[EUR][1000 genomes]
rs62535349	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6474856	1.00[CEU][hapmap]
rs7025956	0.92[CEU][hapmap]
rs7046483	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs923926	0.87[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	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
4	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025566	chr9:14687088-14791199	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1023955	chr9:14754010-14800259	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2761502	chr9:14757877-14827373	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	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
9	nsv892615	chr9:14761260-14782367	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv892616	chr9:14762700-14780698	Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1874109	FREM1	cis	parietal	SCAN
rs1874109	FREM1	cis	cerebellum	SCAN
rs1874109	ZDHHC21	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14745000-14809800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:14748800-14775600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:14748800-14775800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:14748800-14790000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:14752800-14775800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:14755800-14775600	Weak transcription	Fetal Stomach	stomach
7	chr9:14755800-14812400	Weak transcription	Pancreas	Pancrea
8	chr9:14757000-14771800	Strong transcription	Fetal Kidney	kidney
9	chr9:14758400-14793400	Weak transcription	Aorta	Aorta
10	chr9:14760000-14775200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:14763000-14770800	Strong transcription	Fetal Lung	lung
12	chr9:14764800-14809600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:14766600-14787400	Weak transcription	Fetal Intestine Large	intestine
14	chr9:14766800-14775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:14767200-14779200	Weak transcription	Adipose Nuclei	Adipose
16	chr9:14767400-14779000	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:14768000-14773400	Weak transcription	HepG2	liver
18	chr9:14768600-14770800	Weak transcription	Fetal Heart	heart
19	chr9:14768600-14808800	Weak transcription	Fetal Intestine Small	intestine
20	chr9:14768800-14780800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:14769000-14783000	Weak transcription	Colon Smooth Muscle	Colon

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