Variant report

Variant	rs13289925
Chromosome Location	chr9:6483120-6483121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:6482868-6483124	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
UHRF2	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10115883	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10122116	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10124572	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10125914	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10733529	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10758784	0.89[EUR][1000 genomes]
rs10975595	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10975603	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10975605	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1156747	0.80[ASN][1000 genomes]
rs11790625	0.84[ASN][1000 genomes]
rs11791651	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11795355	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12346455	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12347573	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12351293	0.86[ASN][1000 genomes]
rs13283381	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13291472	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13292799	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13296970	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13298500	0.86[ASN][1000 genomes]
rs13301146	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13440427	0.82[ASN][1000 genomes]
rs16924562	0.82[ASN][1000 genomes]
rs16924591	0.87[ASN][1000 genomes]
rs16924624	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16924626	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16924631	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16924634	0.85[ASN][1000 genomes]
rs1870696	0.83[ASN][1000 genomes]
rs33962342	0.84[ASN][1000 genomes]
rs3739654	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4380997	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4384035	0.85[ASN][1000 genomes]
rs4463484	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4556138	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4740844	0.87[EUR][1000 genomes]
rs4740845	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742199	0.86[EUR][1000 genomes]
rs504698	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs530722	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55960819	0.86[ASN][1000 genomes]
rs56396114	0.86[ASN][1000 genomes]
rs569866	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6477086	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6477087	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66509816	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027302	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7029772	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7034328	0.90[ASN][1000 genomes]
rs73399080	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73401025	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7847675	0.89[ASN][1000 genomes]
rs7848831	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7852539	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7860966	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7861073	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7861559	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7873756	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7876000	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	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	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking 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 target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	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
11	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	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
13	esv3415944	chr9:6482061-6486840	Strong transcription Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13289925	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6452600-6488000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:6452800-6485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr9:6452800-6485400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
5	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:6460600-6486800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:6461400-6486000	Weak transcription	K562	blood
8	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
9	chr9:6467400-6486200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:6467400-6497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:6471600-6501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:6471600-6504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:6472200-6497200	Weak transcription	Aorta	Aorta
14	chr9:6472200-6508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:6473000-6491600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:6473000-6499600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:6473800-6498400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:6473800-6506200	Weak transcription	Small Intestine	intestine
19	chr9:6474400-6490600	Strong transcription	HUVEC	blood vessel
20	chr9:6474800-6502800	Strong transcription	Dnd41	blood
21	chr9:6475000-6488400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:6475200-6503000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr9:6475400-6490400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:6475400-6491800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:6475400-6491800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr9:6475400-6494400	Strong transcription	Fetal Thymus	thymus
27	chr9:6475400-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:6475400-6508400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:6475400-6508800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr9:6475400-6508800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr9:6475600-6494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:6475800-6483200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr9:6475800-6484600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:6475800-6488200	Strong transcription	Adipose Nuclei	Adipose
35	chr9:6475800-6491000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr9:6475800-6491800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:6475800-6492000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:6475800-6492800	Strong transcription	GM12878-XiMat	blood
39	chr9:6475800-6493000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:6475800-6493400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr9:6475800-6497200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:6475800-6509000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:6475800-6510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:6476000-6509400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:6476600-6491800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:6476600-6494400	Strong transcription	Osteobl	bone
47	chr9:6477400-6483600	Strong transcription	HSMM	muscle
48	chr9:6477400-6487200	Strong transcription	NH-A	brain
49	chr9:6477400-6488400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:6477600-6483200	Strong transcription	Rectal Mucosa Donor 29	rectum

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