Variant report

Variant	rs13296970
Chromosome Location	chr9:6493297-6493298
allele	A/C
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	chr9:6493224-6493350	K562	blood:	n/a	n/a

Variant related genes	Relation type
UHRF2	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10115883	0.81[EUR][1000 genomes]
rs10122116	0.81[EUR][1000 genomes]
rs10125914	0.80[EUR][1000 genomes]
rs10733529	0.82[EUR][1000 genomes]
rs10758784	0.83[EUR][1000 genomes]
rs10975595	0.84[EUR][1000 genomes]
rs10975605	0.81[EUR][1000 genomes]
rs11791651	0.81[EUR][1000 genomes]
rs12346455	0.89[EUR][1000 genomes]
rs12347573	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13283381	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13289925	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13291472	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13292799	0.83[EUR][1000 genomes]
rs13298500	0.82[ASN][1000 genomes]
rs13301146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924624	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16924626	0.80[EUR][1000 genomes]
rs16924631	0.85[ASN][1000 genomes]
rs16924634	0.82[ASN][1000 genomes]
rs3739654	0.90[EUR][1000 genomes]
rs4380997	0.81[EUR][1000 genomes]
rs4463484	0.80[EUR][1000 genomes]
rs4556138	0.88[EUR][1000 genomes]
rs4740844	0.81[EUR][1000 genomes]
rs4740845	0.81[EUR][1000 genomes]
rs4742199	0.80[EUR][1000 genomes]
rs504698	0.90[EUR][1000 genomes]
rs530722	0.87[EUR][1000 genomes]
rs569866	0.90[EUR][1000 genomes]
rs6477086	0.90[EUR][1000 genomes]
rs6477087	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66509816	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7029772	0.86[EUR][1000 genomes]
rs73401025	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7847675	0.85[ASN][1000 genomes]
rs7848831	0.89[EUR][1000 genomes]
rs7852539	0.89[EUR][1000 genomes]
rs7860966	0.84[EUR][1000 genomes]
rs7861073	0.84[EUR][1000 genomes]
rs7861559	0.84[EUR][1000 genomes]
rs7873756	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13296970	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6458800-6497200	Weak transcription	Colonic Mucosa	Colon
2	chr9:6459400-6501800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:6463600-6518400	Weak transcription	Fetal Brain Male	brain
4	chr9:6467400-6497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:6471600-6501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:6471600-6504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:6472200-6497200	Weak transcription	Aorta	Aorta
8	chr9:6472200-6508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:6473000-6499600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:6473800-6498400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:6473800-6506200	Weak transcription	Small Intestine	intestine
12	chr9:6474800-6502800	Strong transcription	Dnd41	blood
13	chr9:6475200-6503000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:6475400-6494400	Strong transcription	Fetal Thymus	thymus
15	chr9:6475400-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr9:6475400-6508400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:6475400-6508800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:6475400-6508800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr9:6475600-6494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:6475800-6493400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr9:6475800-6497200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:6475800-6509000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:6475800-6510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:6476000-6509400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:6476600-6494400	Strong transcription	Osteobl	bone
26	chr9:6477600-6497800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:6477600-6507800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr9:6477800-6511000	Weak transcription	Fetal Heart	heart
29	chr9:6478000-6498200	Weak transcription	Brain Angular Gyrus	brain
30	chr9:6478200-6498000	Weak transcription	Esophagus	oesophagus
31	chr9:6478400-6503400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr9:6478600-6498600	Weak transcription	Spleen	Spleen
33	chr9:6480200-6508400	Weak transcription	Stomach Mucosa	stomach
34	chr9:6480400-6496600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:6480400-6497400	Weak transcription	Psoas Muscle	Psoas
36	chr9:6481600-6502800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:6483200-6496800	Weak transcription	Right Ventricle	heart
38	chr9:6483200-6498000	Strong transcription	HMEC	breast
39	chr9:6483400-6495400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:6483600-6496800	Weak transcription	HSMMtube	muscle
41	chr9:6484000-6498600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:6484400-6498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:6484600-6497800	Weak transcription	Pancreas	Pancrea
44	chr9:6484600-6501800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:6485800-6498000	Weak transcription	Gastric	stomach
46	chr9:6486600-6495400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:6487000-6497200	Weak transcription	Brain Substantia Nigra	brain
48	chr9:6487000-6497200	Weak transcription	K562	blood
49	chr9:6487200-6493400	Weak transcription	Hela-S3	cervix
50	chr9:6487200-6495600	Weak transcription	Fetal Kidney	kidney

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