Variant report

Variant	rs4878149
Chromosome Location	chr9:27149669-27149670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10967740	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv892863	chr9:27138898-27170934	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4878149	C9orf72	cis	cerebellum	SCAN
rs4878149	ABCC9	trans	parietal	SCAN
rs4878149	SOX15	trans	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27122800-27150800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:27143200-27150000	Weak transcription	Right Atrium	heart
3	chr9:27143800-27150200	Weak transcription	Fetal Lung	lung
4	chr9:27144000-27149800	Weak transcription	Lung	lung
5	chr9:27145400-27150200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:27145400-27150200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:27145400-27150200	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:27145400-27150400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:27145600-27150000	Weak transcription	Adipose Nuclei	Adipose
10	chr9:27145600-27150600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:27145800-27150000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:27147800-27155000	Weak transcription	Aorta	Aorta
13	chr9:27148600-27150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:27149400-27152400	Enhancers	Fetal Stomach	stomach
15	chr9:27149600-27150800	Enhancers	Spleen	Spleen
16	chr9:27149600-27151000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:27149600-27151000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:27149600-27151000	Enhancers	Left Ventricle	heart
19	chr9:27149600-27151800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:27149600-27152000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr9:27149600-27152400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr9:27149600-27152400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr9:27149600-27152400	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:27149600-27152600	Enhancers	Colon Smooth Muscle	Colon
25	chr9:27149600-27154600	Enhancers	HUVEC	blood vessel
26	chr9:27149600-27155400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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