Variant report

Variant	rs7848483
Chromosome Location	chr9:6529677-6529678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UHRF2-3	chr9:6529539-6529917	NONHSAT130138

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10118449	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10975622	0.86[ASN][1000 genomes]
rs10975627	0.88[ASN][1000 genomes]
rs10975629	0.85[ASN][1000 genomes]
rs12000020	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12352034	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13297368	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16924650	0.90[ASN][1000 genomes]
rs2013966	0.80[ASN][1000 genomes]
rs2282158	0.83[ASN][1000 genomes]
rs2297443	0.80[ASN][1000 genomes]
rs34551978	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34806087	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35458135	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818705	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	esv2761298	chr9:6505897-6544766	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv934176	chr9:6517535-6644738	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv892163	chr9:6523056-6632061	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1025627	chr9:6523056-6648098	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
16	nsv613206	chr9:6525753-6686738	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
17	esv3324686	chr9:6528411-6728310	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7848483	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6498800-6554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:6506400-6530600	Weak transcription	Gastric	stomach
3	chr9:6507000-6534400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:6508400-6530600	Weak transcription	Left Ventricle	heart
5	chr9:6508600-6537800	Weak transcription	HMEC	breast
6	chr9:6508600-6538200	Weak transcription	NHEK	skin
7	chr9:6509800-6530200	Weak transcription	A549	lung
8	chr9:6510400-6558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:6510600-6543000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:6518000-6530400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:6522000-6549200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:6522400-6530400	Weak transcription	NHDF-Ad	bronchial
13	chr9:6522400-6531600	Weak transcription	GM12878-XiMat	blood
14	chr9:6523000-6538400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:6523400-6532200	Weak transcription	Aorta	Aorta
16	chr9:6523600-6530400	Weak transcription	HUVEC	blood vessel
17	chr9:6524000-6530400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:6525400-6530400	Weak transcription	Ovary	ovary
19	chr9:6525800-6530200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:6526000-6530200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:6526000-6530200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:6526000-6530200	Weak transcription	Osteobl	bone
23	chr9:6526000-6538600	Weak transcription	NH-A	brain
24	chr9:6526200-6530400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:6526200-6530400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:6526200-6530400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:6526200-6532600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:6526400-6532000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:6527200-6530400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:6527400-6530400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:6528200-6543200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr9:6528400-6530400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:6528400-6534800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:6528400-6548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:6528600-6530200	Weak transcription	Pancreas	Pancrea
36	chr9:6528600-6532000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:6528600-6532200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:6528600-6534600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:6528600-6558000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:6528800-6534600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:6529200-6530000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:6529200-6533000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:6529400-6548400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:6529600-6531200	Strong transcription	Liver	Liver
45	chr9:6529600-6531800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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